title: LPS-60min rep 2

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
nascent RNA
bone marrow derived macrophage treated with LPS-60min rep 2

data_processing:
Basecalls performed using CASAVA version 1.7
PolyA stretches at the end of the reads were clipped using HOMER v4.7 (command: homerTools trim -3 AAAAAAAAAAAA fastqfile)
Trimmed reads were aligned to the mouse genome (mm9) using bowtie2 v2.0.5.  Only reads with a single best alignment were kept for downstream analysis.
Downstream analysis of GRO-Seq data was carried out using HOMER (v4.6, http://homer.salk.edu/homer/).  This includes calculation of gene expression FPKM levels, identification of transcripts, generation of Genome Browser bedGraphs, etc.  Gene expression values were generated by HOMER using RefSeq gene models, and are calculated across the entire gene body (exons+introns).
Genome_build: mm9
Supplementary_files_format_and_content: Text (tab-delimited) file containing FPKM for all experiemnts.  Columns: 1) RefSeq ID, 2) chromosome, 3) start, 4) end, 5) strand, 6) length, 7) copies in genome, 8) annotation, 9 on) experiment FPKM

organism: Mus musculus

source_name: Bone marrow

growth_protocol: All primary macrophages were differentiated from bone marrow isolated from an isogenic C57 background as described previously (Barish et al. 2010)

extract_protocol:
Nuclei were isolated from primary macrophages and subjected to nuclear run-on in the presence of BrUTP. BrUTP incoorporated nascent RNAs were isolated using anti-BrU antibodies (Santa Cruz, sc-32323 AC) for the construction of sequencing libraries.
GRO-Seq library generation was carried out as described previously (Hah et al. 2013) from two biological replicates of mouse primary macrophages treated with LPS alone or with LPS and DEX as indicated.  GRO-Seq libraries were sequenced on an Illumina HiSeq2000 sequencer to a depth of over 50 million reads per library.

treatment_protocol: The primary macrophages were plated for experiments in macrophage serum-free media (Invitrogen) prior to treatment with 100 ng/ml LPS (Sigma-Aldrich) for the time indicated, without or with 1µM Dexamethasone (Sigma-Aldrich).

tag: source mice

value: 8 weeks

value: male

value: bone marrow derived macrophage

tag: treatment

value: 100 ng/ml LPS

tag: library strategy

value: GRO-Seq

tag: time

value: 60 min


title: LPS-60min rep 1

status: Public on Dec 25 2014

type: SRA

city: La Jolla

country: USA

description:
nascent RNA
bone marrow derived macrophage treated with LPS-60min rep 1

library_source: transcriptomic

molecule: total RNA

tag: age

tag: gender

tag: cell type


title: LPS-20min rep 2

description:
nascent RNA
bone marrow derived macrophage treated with LPS-20min rep 2

value: 20 min


title: LPS-20min rep 1

description:
nascent RNA
bone marrow derived macrophage treated with LPS-20min rep 1


title: LPS-180min rep 1

description:
nascent RNA
bone marrow derived macrophage treated with LPS-180min rep 1

value: 180 min


title: LPS-0min rep 2

description:
nascent RNA
bone marrow derived macrophage treated with LPS-0min rep 2

value: no treatment

value: 0 min


title: STT6838_GIST430WT_nutlin10µM

city: Stanford

first: Xiangqian

last: Guo

state: CA

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

description: Experiment type: 3SEQ

data_processing:
Sequenced Reads after filtered by quality, were re-filtered by fastx, and then were mapped to the transcriptome (refMrna, downloaded from the UCSC genome browser, www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches
Total numbers of sequenced reads for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix. The library size was then normalized to one million reads (TPM).
The sequencing depth for each library was determined with the estimation of library saturation for transcriptome detection, which showed that our sequencing depths were deep enough to detect almost all of the known mRNAs expressed.
The distances between sequencing reads and 3’end of mRNAs were measured to be around 100-200nt as we expected.
Genome_build: hg19
Supplementary_files_format_and_content: expressional matrix with sample by column and gene by row

molecule: polyA RNA

organism: Homo sapiens

source_name: GIST430, nutlin10µM

extract_protocol:
Total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
Poly(A)+RNA was selected and enriched with oligo(dT) using the Oligotex mRNA mini Kit (Qiagen).  The Poly(A) RNA was heat sheared to 100~200nt fragments. The sheared RNA was then subjected to first and second strand cDNA synthesis, followed by additional steps of library construction as described previously. The libraries were sent to the Stanford Genomic Center to be sequenced for the first 36bp at the 5’end of mRNA fragments with Illumina machines.

treatment_protocol: GIST430 cells were treated with DMSO solvent control, nutlin-3 2.5μM, or nutlin-3 10μM for 18h in three independent experiments to obtain triplicates for significance analyses.

tag: cell line

tag: tissue type

value: Gastrointestinal Stromal Tumor

tag: tissue

value: Soft Tissue

tag: tissue archive method

value: Fresh


title: STT6848_GIST430WT_DMSO

description: Experiment type: 3SEQ

source_name: GIST430, DMSO


title: STT6850_GIST430WT_nutlin10µM

description: Experiment type: 3SEQ


title: LPS-180min rep 2

description:
nascent RNA
bone marrow derived macrophage treated with LPS-180min rep 2


title: STT6826_GIST430WT_nutlin10µM

description: Experiment type: 3SEQ


title: STT6837_GIST430WT_nutlin2.5µM

description: Experiment type: 3SEQ

source_name: GIST430, nutlin2.5µM


title: STT6849_GIST430WT_nutlin2.5µM

description: Experiment type: 3SEQ


title: LPS-0min rep 1

description:
nascent RNA
bone marrow derived macrophage treated with LPS-0min rep 1


title: STT6824_GIST430WT_DMSO

description: Experiment type: 3SEQ


title: STT6825_GIST430WT_nutlin2.5µM

description: Experiment type: 3SEQ


title: EpiSC with BMP4, 48h

status: Public on Dec 24 2014

city: Rotterdam

first: Dorota

last: Kurek

address: Dr Molewaterplein 50

country: Netherlands

institute: ErasmusMC

description: I13-1190-03-48hFAB_ATTCCT_L001_R1_MERGED

data_processing:
Raw files were groomed using FASTQ Groomer into sanger reads, then aligned using Tophat2 v2.0.9 to the reference genome mm9, using preSet settings.
Transcripts were assembled in Cufflinks v2.1.1, with a max intron length of 300000, a min isoform fraction of 0.1, a pre MRNA fraction of 0.15, with no quartile normalization or bias correction, with multi-read correct and effective length correction.
Transcripts were merged in Cuffmerge using mm9 as a reference genome. FPKM values were called in Cuffdiff, classic-fpkm as a library normalization method, a blind dispersion estimation method, a FDR of 0.05, with a min alignment count of 10, with multi-read correction.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file, includes FPKM values for each sample

source_name: EpiSC

extract_protocol:
Total RNA was prepared using TriPure (Roche) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using the Illumina TruSeq v3 protocol

tag: strain background

value: epiblast stem cells (EpiSC)

tag: treated with

value: BMP4 for 48h


title: EpiSC with IWP2, 48h control

value: IWP2 for 48h (control)


title: sham

city: Beijing

first: Shouyu

last: Yan

address: 5#, Yiheyuan Road

department: Institution of Molecular Medicine

country: China

institute: Peking University

data_processing:
Sequenced reads were filtered by in-house pipeline to remove low-quality and unclear base containing reads, then mapped to danRer7 by tophat v1.4.0 with parameters --mate-inner-dist 100 --solexa1.3-quals --coverage-search --microexon-search --library-type fr-firststrand
Differential expression were performed by Cuffdiff v2.0.2 with paremeters --compatible-hits-norm --multi-read-correct --library-type fr-firststrand
Genome_build: danRer7
Supplementary_files_format_and_content: Table format as Cuffdiff results.

organism: Danio rerio

source_name: heart

extract_protocol:
total RNA was extracted using QIAGEN RNeasy Microarray Tissue Mini Kit (Cat No. 73304)
Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions. A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed; Exome fragments were captured and enriched by SureSelect Human All Exon 50 Mb kits (Agilent Technologies) following the manufacture’s protocol.

value: heart

tag: developmental stage

value: adult

tag: strain

value: TL


title: EpiSC with IWP2 T=0

value: IWP2 T=0


title: EpiSC with BMP4 and IWP2, 48h

description: I13-1190-02-48hFABI_ACTGAT_L001_R1_MERGED

value: BMP4 and IWP2 for 48h


title: S2 repB_4hr

city: Tallahassee

first: Jonathan

middle: H

last: Dennis

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State Unversity

library_source: genomic

data_processing:
Illumina adapters were clipped from the 3' ends of reads with cutadapt 1.7.
MNase-seq reads were aligned to the Drosophila reference genome UCSC.dm3 using bowtie2 2.1.0
Bed files correspond to inferred fragment coordinates based on concordant mate-pair alignments to the dm3 reference assembly
Genome_build: UCSC.dm3
Supplementary_files_format_and_content: bed files include genome-wide nucleosome positions for each sample

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were maintained at 28oC in Schneider's Drosophila medium (Invitrogen), supplemented with 10% heat inactivated fetal bovine serum (Life Technologies).

extract_protocol:
MNase-digested DNA samples were resolved on 2% agarose gel. DNA band containing mononucleosomal DNA (<=200bps) was excised and purified by the freeze-squeeze method.
Libraries of mononucleosomal DNA were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), starting with 30ng of mononucleosomal DNA for each reaction. The samples were end-prepared, adaptor-ligated and indexed (NEB #E7335S/L, NEB #E7500S/L) according to the manufacturer’s instructions, followed by purification with AMPure XP beads (Beckman Coulter, Inc. #A63881) without size selection. The quantity and quality of the library were checked with Qubit 2.0 Fluorometer (Life Sciences) and Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were quantified using KAPA Library Quantification (KK824).  Resulting libraries were plated using the Illumina cBot and run on the Illumina HiSeq 2500 platform configured for 50 bp paired-end reads.

treatment_protocol: Heat killed S. typhimurium was added to S2 cells at a final concentration of 107 cells/ml. S2 cells were harvested at 0, 30 minutes, 1 hour, and 4 hours after stimulation at 3 × 107 S2 cells each time point, formaldehyde crosslinked and digested with 40U/ml MNase.

value: hemocyte-like cell line S2

value: heat-killed Salmonella typhimurium stimulation


title: EpiSC with Wnt3a, 48h

value: Wnt3a for 48h


title: S2 repB_1hr


title: 7dpa


title: S2 repB_0hr

value: control


title: S2 repA_4hr


title: S2 repA_0hr


title: STT6836_GIST430WT_DMSO

description: Experiment type: 3SEQ


title: S2 repA_1hr


title: S2 repA_0.5hr


title: MGA3_PRIM

city: Bielefeld

first: Marta

last: Irla

address: Universitätsstraße 25

department: Genetics of Prokaryotes

country: Germany

institute: Bielefeld University

data_processing:
Sequencing was performed in single-read mode with 50 nt read length for the enriched 5’‑ends cDNA library and in paired-end mode with 25 nt read length for the whole transcriptome cDNA library. The base calling was realized with the Illumina instrument software.
The last bases of all sequence reads from the enriched 5’‑ends approach were trimmed to a final length of 20 nt. Next, these trimmed reads were mapped to the B. methanolicus MGA3 reference sequences using the exact mapping algorithm SARUMAN (Blom et al. 2011, Bioinformatics) and allowing a single mismatch to occur in the alignment of each read. In case of the reads belonging to the whole transcriptome RNA-seq data set, the forward and reverse read were combined to one read, containing the reference sequence as an insert, if both reads were present and in inverse orientation in a maximal distance of 1 kb to each other. Sequence reads not fulfilling this criterion were retained as single mapping reads. Paired mappings with a distance larger than 1 kb were discarded from subsequent analyses.
For the visualization of the mapped short reads, the Java software ReadXplorer (Hilker et al. 2014, Bioinformatics) was used.
The identification of putative transcription start sites was performed based on the method described previously (Pfeifer-Sancar et al. 2013, BMC Genomics), but with a recently developed transcriptome analysis module which will be integrated into the software ReadXplorer in the near future (Hilker et al. 2014, Bioinformatics)
Genome_build: GenBank accession no. CP007739, CP007740 and CP007741.
Supplementary_files_format_and_content: Excel files include TSS, operons and logRPKM values.

organism: Bacillus methanolicus

source_name: cell culture

growth_protocol: Cells were cultivated in 16 different conditions; 13 cultivations in bioreactors and 3 cultivations in shake flasks.

extract_protocol:
For the extraction of total RNA the NucleoSpin RNA isolation kit (MACHEREY-NAGEL, Düren, Germany) and the RNase-free DNase set (QIAGEN, Hilden, Germany) were used according to the manufacturer’s instructions. The total RNA was isolated individually for each cultivation condition. The quality and quantity of the isolated RNA was assessed by PCR with gene-specific primers (Supplementary Table 1) and with capillary gel electrophoresis (Agilent Bioanalyzer 2100 system using the Agilent RNA 6000 Pico kit; Agilent Technologies, Böblingen, Germany). The extracted RNA samples were pooled in equal parts and the pool of total RNA was subsequently used for the preparation of two different cDNA libraries.
The cDNA libraries of B. methanolicus MGA3 were prepared according to two different protocols. One approach focused on the enrichment of 5’‑ends of primary transcripts, while the other method allowed the analysis of the whole transcriptome. Both cDNA library preparation protocols have been previously described in detail  (Pfeifer-Sancar et al. 2013, BMC Genomics). In the present study, the experimental workflow was changed at two steps. The first difference is that the amplification of cDNA fragments was customized by adding the PCR additive betaine to a final concentration of 2.7 M in each PCR reaction. Secondly, after cDNA amplification the two libraries were purified and size-selected via gel electrophoresis for fragment sizes between 100 and 800 bp.

tag: library preparation

value: 5'end enriched


title: D3T7HLA

status: Public on Dec 23 2014

city: Cambridge

first: Magali

last: Soumillon

state: MA

address: Divinity Avenue 7

institute: Harvard University, HSCRB

description:
Differentiation 3, full confluency
D3_Lipid_UMI.dat

data_processing:
Mapping of read2 on mRNA refseq using BWA
Parsing the output based on cell barcode stored in read1 (first 6bp)
Gene expression computation based on Unique Molecular Identifier (UMI) counts stored in read1 (base 7 to 16)
Concatenation of single cell gene expression in gene expression matrices (processed data files)
Genome_build: hg19
Supplementary_files_format_and_content: gene expression matrix

source_name: Human Adipose Derived Stem Cells

growth_protocol: Human adipose-derived stem cells were isolated from lipoaspirate and purified by flow-cytometry (positive CD29, CD44, CD73, CD90, CD105, CD166; negative CD14, CD31, CD45, Lin1) (Life Technology, lot 2117). Cells were grown in a 2% reduced serum medium (MesenPro RS - Life Technologies) and expanded for no more than 3 passages.

extract_protocol:
Cells were harvested using TrypLE Express (Life Technologies) and medium removed by pelleting the cells (5 min at 1000 rpm). RNA was immediately stabilized by resuspending the cells in RNAprotect Cell Reagent (Qiagen) and RNaseOUT Recombinant Ribonuclease Inhibitor. (1:1000, Life Technologies). Prior to sorting, cells were diluted in PBS, pH 7.4 (no calcium, no magnesium, no phenol red, Life Technologies) and stained for viability using Hoechst 33342 (Life Technologies). 384-well capture plates were filled with 5µl of diluted Phusion HF buffer (1:500, New England Biolabs). Cells were sorted individually in each well of the 384-well capture plates using a FACSAria II flow cytometer (BD Biosciences) based on Hoechst DNA staining. After sorting, plates were immediately sealed, spin down and frozen on dry ice. Sorted cells were stored at -80°C. For lipid content based single cell sorting, cells were stained with HSC LipidTOX Neutral Lipid Stain (Life Technologies) and sorted according to their relatively “high” or “low” lipid content (upper/lower 20% or 50%). For bulk SCRB-Seq, populations of both unsorted and sorted cells were lysed in QIAzol (Qiagen) and RNA was extracted and purified using Direct-zol RNA MiniPrep (Zymo Research).
Single Cell RNA Barcoding and Sequencing (SCRB-Seq), 3’ Digital Gene Expression (3’ DGE)

treatment_protocol: At 80% confluency (1st differentiation) or two days after confluency (2nd differentiation), the cells were induced towards an adipogenic fate by switching from growth medium to the StemPro adipogenesis differentiation medium (Life Technologies). Cells were fed every three days during the 14 days of differentiation.

tag: starting material

value: single cells

tag: differentiation

value: Differentiation 3, full confluency

tag: sorting#

value: Hoechst + LipidTOX, "high lipid" fraction (upper 50%)

tag: scrb-seq variant#

value: Proteinase K + Maxima

tag: time point

value: Day 7


title: D3T7HLB


title: D3T7_sorted

description:
Differentiation 3, full confluency
D3_Bulk_UMI.dat

value: extracted RNA

value: FACS to tube

value: Bulk


title: D3T14_unsorted

value: No FACS

value: Day 14


title: D3T3_unsorted

value: Day 3


title: S2 repB_0.5hr

tag: treatment

tag: time


title: D3T7HLC


title: D3T7_unsorted


title: D3T14_sorted


title: D3T3_sorted


title: EpiSC with Wnt3a and BMP4, 48h

tag: cell type

value: epiblast stem cells (EpiSC)

value: Wnt3a and BMP4 for 48h


title: D3T7LLC

value: Hoechst + LipidTOX, "low lipid" fraction (lower 50%)


title: D3T3B

description:
Differentiation 3, full confluency
D3_UMI.dat

value: Hoechst only


title: D3T7LLA


title: D3T7B


title: D3T0C

value: Day 0


title: D3T7C


title: D3T7LLB


title: D3T0_unsorted


title: D3T3A


title: D3T7A


title: D2T14HLC

description:
Differentiation 2, full confluency
D2_UMI.dat

value: Differentiation 2, full confluency

value: Hoechst + LipidTOX, "high lipid" fraction (upper 20%)

value: SmartScribe


title: D3T0B

value: single cells

value: Differentiation 3, full confluency


title: D3T0A

value: Proteinase K + Maxima


title: D2T14HLB


title: D2T14LLC

value: Hoechst + LipidTOX, "low lipid" fraction (lower 20%)


title: D2T14HLA


title: MGA3_WT

value: whole transcriptome


title: D2T14LLB


title: D3T3C


title: D2T14LLA


title: gpc-a1_gpc-b2_22DAA_Rep_3

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

data_processing:
Bases were called at the UC Davis Genome Center using CASAVA1.5
Raw reads were trimmed for quality using fastq-quality-trimmer (http://hannonlab.cshl.edu/fastx_toolkit/, default options, except -t 20, -l 25).
Trimmed reads were mapped to a reference set of genomic contigs from the hexaploid wheat variety ‘Chinese Spring’. This reference was assembled from flow-sorted A and B chromosomes and provided by the International Wheat Genome Sequencing Consortium (http://plants.ensembl.org/Triticum_aestivum/Info/Index). Reads were aligned using GSNAP(l) (version 05-09-2013, default parameters except -m 2 -n 1 -N 1 -A sam).
Uniquely mapped reads were counted with ht-seq count (-m union) (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) using a custom-made GFF file describing 139,828 transcribed genomic loci.
Gene loci with a low number of counts were excluded using the R script "noleaven" (http://topherconley.github.io/noleaven/).
Genome_build: http://wheat-urgi.versailles.inra.fr/Seq-Repository
Genome_build: http://plants.ensembl.org/Triticum_aestivum/Info/Index

organism: Triticum turgidum subsp. durum

growth_protocol: Plants were grown in a greenhouse at UC Davis, CA, under standard conditions.

extract_protocol:
Total RNA was extracted from flag leaves using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
RNA-seq libraries were constructed using the TruSeq™ RNA sample preparation kit v1 (Illumina, San Diego, CA) according to the manufacturer's instructions and their quality determined by running samples on a high-sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genotype/variation

value: 22 days after anthesis

value: Flag leaf


title: gpc-a1_gpc-b2_HD_Rep_3

value: heading date


title: gpc-a1_gpc-b2_12DAA_Rep_2

value: 12 days after anthesis


title: gpc-a1_gpc-b2_12DAA_Rep_3


title: gpc-a1_gpc-b2_22DAA_Rep_2


title: gpc-a1_gpc-b2_22DAA_Rep_4


title: gpc-a1_gpc-b2_12DAA_Rep_1


title: gpc-a1_gpc-b2_12DAA_Rep_4


title: gpc-a1_gpc-b2_22DAA_Rep_1


title: gpc-a1_gpc-b2_HD_Rep_4


title: gpc-a1_gpc-b2_HD_Rep_2


title: gpc-a1_22DAA_Rep_2


title: gpc-a1_12DAA_Rep_1


title: gpc-a1_22DAA_Rep_1


title: gpc-a1_22DAA_Rep_4


title: gpc-a1_22DAA_Rep_3


title: gpc-a1_HD_Rep_4


title: gpc-a1_12DAA_Rep_4


title: gpc-a1_12DAA_Rep_2


title: gpc-a1_HD_Rep_3


title: WT_22DAA_Rep_4

value: wild type


title: gpc-a1_HD_Rep_1


title: gpc-a1_12DAA_Rep_3


title: gpc-a1_HD_Rep_2


title: D3T0_sorted

value: extracted RNA

value: FACS to tube

value: Bulk


title: WT_22DAA_Rep_2


title: WT_22DAA_Rep_1


title: gpc-a1_gpc-b2_HD_Rep_1


title: WT_12DAA_Rep_4


title: WT_12DAA_Rep_3


title: WT_12DAA_Rep_2


title: WT_HD_Rep_4


title: WT_HD_Rep_2


title: RRBS of 129 EpiSCs reverted to a naïve state

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
129_naive
RRBS

data_processing:
FASTQ files were generated using the Illumina CASAVA 1.8.2 software.
The plasmid introduces a CTAGANNNNNNATTGATT prefix at one read and an AATTCAATT prefix on the other read (were NNNNNN is the UMI). These prefixes were removed and the UMI recorded for each fragment. A small fraction of reads include longer prefixes that result from amplicons that did not undergo digestion by XbaI or EcoRI. These reads were identified and the longer prefixes were removed as well.
The reads were aligned to the mm9 reference genome using bismark version 0.7.7. Alignment was performed independently for each read of the read-pair. We expect each read to start at an MspI restriction site. Therefore we discarded reads that failed to align within 1bp of such sites. We also discarded read-pairs where each read aligned to remove MspI sites. On the other hand, in cases where one read uniquely mapped on a restriction site but its pair could not be mapped uniquely or could not be mapped at all, we attempted to re-align the entire read pair to the fragment.
To avoid PCR biases we grouped reads that map to the same MspI restriction site, have the same UMI and were ligated into the plasmid in the same orientation (positive or negative). Only the first such read was maintained and all other reads were dropped.
The methylation state of each CpG was extracted from the bismark output. For each CpG, the number of reads in which it was methylated or unmethylated was counted and recorded.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text files containing CpG methylation values. The files' columns are: Column1: chromosome. Column 2: position of CpG. Column 3: seen count. Column 4: methylation count. Note that each CpG's coverage is given by column 3, and its methylation value by column4/column3. Files ending with _orig.cpgs.txt represent the data used in the paper. Files ending with _new.cpgs.txt represent the output of a newer, improved version of our computational pipeline.

source_name: 129 EpiSCs

growth_protocol: All cells were grown in N2B27-based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen), 5ml B27 supplement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM b-mercaptoethanol (Sigma), penicillin/streptomycin (Invitrogen), 5 mg/ml BSA (Sigma).  Primed EpiSCs were grown in N2B27 with 8ng/ml recombinant human bFGF (Peprotech Asia), 20 ng/ml recombinant human Activin (Peprotech Asia) and 1% KSR. The EpiSCs were grown on feeder-free gelatin/vitronectin- or Matrigel-coated plates.  Primed EpiSCs were reverted into a naive state by growing them 2i/LIF conditions: N2B27 with 5ug recombinant human LIF (Peprotech), 3mM CHIR99021 ( Axon Medchem) and 1mM PD0325901 (TOCRIS). Naive cells were grown on gelatin-coated plates.

extract_protocol:
Genomic DNA was extracted from snap-frozen cell pellets (Quick-gDNA MiniPrep, Zymo Research). 300ng of DNA was then digested overnight with MspI (NEB R0106) followed by end-repair (NEB E6050) and addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The resulting DNA fragments were size-selected for ones shorter than 500bp using AMPure XP beads (Beckman Coulter A63881). 10ng of size-selected DNA was ligated, using quick T4 ligase (NEB M2200), into a cut and T-tailed plasmid containing a 6bp unique molecular identifier (UMI) sequence. The ligated plasmid was bisulfite converted and cleaned (EZ DNA methylation Gold kit, Zymo Research). The converted DNA was amplified using 25 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching specific locations on the plasmid. The primer sites were cut from the amplicons using XbaI (NEB R0145) end EcoRI-HF (NEB R3101). Further details regarding the plasmid are available in Shipony Z et al. Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells. Nature 2014 Sep 4;513(7516):115-9.
RRBS fragments underwent addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The fragments were then ligated to Illumina compatible adapters using quick T4 ligase (NEB M2200) and amplified using 8 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching the Illumina adapters. The final products underwent gel electrophoresis using NuSieve 3:1 agarose (Lonza 50094). Gel bands matching fragment sizes of 200-500bp were cut and the DNA was extracted (MinElute Gel Extraction Kit, Qiagen 28604). Libraries were then pooled and sequenced on HiSeq 2500 system according to the manufacturer’s procedures.

tag: cell line

value: EpiSC

tag: pluripotent state

value: Naïve


title: WT_HD_Rep_3

tag: tissue


title: WT_HD_Rep_1


title: RRBS of primed 129 EpiSCs

description:
129_primed
RRBS

value: Primed


title: WT_12DAA_Rep_1


title: Whole-cell-extract of primed WIS2 ES stem cells

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to hg19 reference genome using bowtie version 1.0.0. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read (flags -a -m 1 --best --strata -v 1)
To rule out sequencing depth bias, the aligned sequences were down-sampled such that all samples had the same number of aligned reads. Human samples of the marks H3K4me3, H3K27me3, H3K4me1 and H3K27ac, as well as whole-cell extract, were down-sampled to include 3,750,000 aligned reads. H3K9me3 samples were down-sampled to 5,900,000 aligned reads.
Peaks were detected with MACS version 1.4.1, with whole-cell-extract used for control
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain enriched peaks detected by MACS version 1.4.1

source_name: human ICM-derived ES cell line

growth_protocol: Primed Cells were expanded in DMEM/F12, 20%KSR and 8ng/ml FGF2 on irradiated Feeder cells.  Rock inhibitor was added 2-24 hours before splitting with trypsin. Naïve cells were expanded for 20 days in WIS-NHSM conditions that include:  KO-DMEM (Invitrogen 10829-018) 03-049)  - 500ml, - Pen-strep 5ml (Biological Industries 03-033-1B), - L-glutamine 5ml (Biological Industries - 02-022-1B), - NEAA – 5ml (Biological Industries 01-340-1B), - 5gr Albumax I (Invitrogen - 11020021) (dissolve in media bottle for 30 minutes in RT)  - Insulin (Sigma I-1882) - add 6.25mg insulin per 1 bottle to give approximately additional 12.5microg/ml insulin)  -   Apo-transferrin (Sigma T-1147), 100 μg/ml final concentration  -  Progesterone (Sigma P8783), 0.02 μg/ml final concentration;  - Putrescine (SigmaP5780), 16 μg/ml final concentration  -  Sodium selenite (Sigma S5261), add 5 μl of 3 mM stock solution per 500ml of medium.  - L-ascorbic acid 2-phosphate (Sigma  A8960) (50 μg/ml final concentration)    - 1) human LIF (in house produced or Peprotech # 300-05) – 10 μg total  (~20ng/ml final concentration) (2 viles)  - 2) FGF2 (Peprotech 100-18c or Rnd systems –4114-TC-01M) 8ng/ml final (1 vile)  - 3) TGFB1 – 1ng/ml final (Peprotech 100-21c-1000) (0.5 vile)  - 4) Chir99021 (Axon 1386)– 3μM final (1/3 vile)  - 5) PD0325901 (Axon 1408)– 1μM final (1 vile)  - 6) p38i BIRB796 (Axon 1358)– 2μM final(1 vile)  - 7) JNKi SP600125 (TOCRIS 1496)– 5μM final (1 vile).  -  8) ROCKi Y27632 (Axon 1683)-10μM final (2 viles or add fresh 1:1000 every media change)   - 9) PKCi (Go6983 – TOCRIS 2285)- 0.5μM (1 vile or add 1:2000 fresh every media change)

extract_protocol:
 Approximately 40 × 106 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature), and then quenched with glycine (5 min at room temperature). Fixed cells were lysed in 50 mM HEPES KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4 °C (Roche), centrifuged at 950g for 10 min and resuspended in 0.2% SDS, 10 mM EDTA, 140 mM NaCl and 10 mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at −4 °C to size ranges between 200 and 800 bp, and precipitated by centrifugation. 10 μg of each antibody was pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 h at room temperature. Beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250 mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65 °C. Eluate was treated sequentially with RNase A (Roche) for 30 min and proteinase K (NEB) for 2 h, and then incubated at 65 °C for 4 h. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881)
140ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed twice on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 100ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 12 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer and KAPA HiFi matermix) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

tag: chip antibody

value: WCE

value: ICM-derived WIS2

value: ESCs


title: WT_22DAA_Rep_3


title: control

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequence were trimed by our Perl scripts.
Supplementary_files_format_and_content: tab-delimited text files including sequences and their counts

source_name: HT-29 cells

growth_protocol: Human intestinal epithelial cells (HT-29) were maintained at 37°C in a humidified 5% CO2 incubator with RPMI-1640 medium (Gibco, Carlsbad, CA) containing 10% foetal bovine serum (FBS) (Gibco), 100 units/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: total RNA was extracted from Salmonella strain SE2472-infected HT-29 cells (which were lysed with PBS containing 0.1% Triton X-100, centrifuged to remove cell debris, and filtered through a 0.22-μm membrane) using TRIzol LS reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: sample 1 (control): HT-29 cells were treated with PBS as mock infection. Sample 2 (SE infection): HT-29 cells were infected with salmonella strain SE2472.

tag: infection


title: Whole-cell-extract of naïve WIS2 ES stem cells


title: H3K27ac marks of naïve WIS2 ES stem cells

value: anti-H3K27acetyl (ab4729, Abcam)


title: H3K4me1 marks of naïve WIS2 ES stem cells

value: anti-H3K4me1 (ab8895, Abcam)


title: H3K27me3 marks of primed WIS2 ES stem cells

value: anti-H3K27me3 (07-449, Millipore)


title: H3K27me3 marks of naïve WIS2 ES stem cells


title: Whole-cell-extract of primed LIS2 ES stem cells

value: ICM-derived LIS2


title: H3K4me1 marks of primed WIS2 ES stem cells


title: H3K4me3 marks of naïve WIS2 ES stem cells

value: anti-H3K4me3 (ab8580, Abcam)


title: H3K4me3 marks of primed WIS2 ES stem cells


title: H3K4me3 marks of primed LIS2 ES stem cells


title: H3K9me3 marks of primed WIS2 ES stem cells

value: anti-H3K9me3 (ab8898, Abcam)


title: H3K4me1 marks of primed LIS2 ES stem cells


title: H3K9me3 marks of naïve LIS2 ES stem cells


title: H3K27ac marks of primed WIS2 ES stem cells


title: Whole-cell-extract of naïve LIS2 ES stem cells


title: H3K4me3 marks of naïve LIS2 ES stem cells


title: SE infection

source_name: Salmonella enteritidis strain SE2472 infected HT-29 cells

value: Salmonella enteritidis strain SE2472


title: H3K4me1 marks of naïve LIS2 ES stem cells


title: H3K27ac marks of primed LIS2 ES stem cells


title: H3K9me3 marks of primed LIS2 ES stem cells


title: H3K27ac marks of naïve LIS2 ES stem cells


title: Input 2

city: Chicago

first: Ann

last: Harris

state: IL

address: 2430 N Halsted Street  Box 211

department: Human Molecular Genetics

institute: Lurie Children's Hospital of Chicago Research Center

data_processing:
Fastq files were aligned to the hg19 version of the human genome using Bowtie (v 1.0.0) with a seed length of 40 and a maximum number of 3 mismatches allowed in the seed. Only unique reads were used. The --best argument was used.
Using Homer (v 1.2) software, tag directories were created using the makeTagDirectory command with default settings.
Using Homer (v 1.2) peaks were called using the findPeaks command with an FDR of .01, factor/histone style (see sample column), input tag directory as control library (see sample column), and all other settings as default.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing locations of EHF binding peaks

source_name: Lung adenocarcinoma cells

growth_protocol: Calu-3 cells were grown in DMEM/Low glucose supplemented with 10% FBS.

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPEs pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)).  Nuclear preparation was isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibody.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. DNA was then incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were ligated to the ends and converted to dsDNA using 5 cycles of PCR.  DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles.  DNA was purified with 1.2x AMPusreXP beads. Sequencing was preformed on an Illumina Hi-Seq.

value: Lung adenocarcinoma

value: none (input)


title: EHF ChIP-seq replicate 2

value: EHF (Clone 5A.5), Pierce

tag: -style parameter used for homer peak calling

value: factor

tag: input used for homer peak calling

value: Input 1


title: Calu-3 Dnase-seq

description: DNAse-Seq

data_processing:
Bowtie v 1.0.0 used for alignment
Sequences are mapped to hg19 reference genome with parameters:  -q -m 1 -l 20 -n 3 --best --strata  --chunkmbs 256 -p 10
The peak calls for the DNase-seq data were made with the F-seq application to give a discrete number of DHS within the REP cells. These sites were determined by F-seq by fitting the data to a gamma distribution to calculate p-values. P-values below a 0.05/0.01 threshold in contiguous regions were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing the locations of DNase hypersensitive sites

extract_protocol:
genomic DNA is digested with different concentrations of DNaseI (NEB) and purified for library construction
DNase-seq libraries were prepared using the Crawford lab method

value: lung adenocarcinoma


title: H3K4me1 ChIP-seq

value: H3K4Me1 (ab8895, Abcam)

value: histone

value: Input 2


title: EHF ChIP-seq replicate 1


title: H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: H3K9me3 marks of naïve WIS2 ES stem cells

value: ICM-derived WIS2

value: ESCs


title: Input 1


title: H3K27me3 marks of primed LIS2 ES stem cells

value: anti-H3K27me3 (07-449, Millipore)


title: A549 EHF-overexpressing clone 30 rep 3

data_processing:
Paired-end reads (100bp) format were mapped to the reference human genome (hg19) with ENSEMBL Release 74 of human genome annotation as transcriptome mapping, using TopHat (v2.0.10)
The aligned reads were then processed by Cufflinks (v2.1.1) to assemble expressed genes and transcripts against the UCSC hg19 gene structure annotation, and estimate expression levels for each transcript.
The assembly files for each of the samples (10 for EHF knockdown, 23 for EHF overexpression)  were then merged to create a single transcriptome annotation and differentially expressed genes identified by Cuffdiff.
Samples were then normalized and expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) and both a test statistic (p-value) and an adjusted p-value (q-value) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene and fold difference between control and EHF siRNA samples and fold difference between control and pCDNA-EHF samples.

source_name: lung carcinoma cells_overexpression_EHF

growth_protocol: Calu-3 and A549 cells were grown in DMEM/Low glucose supplemented with 10% FBS.

extract_protocol:
TRIzol® (Life Technologies) used for RNA extraction.
RNA libraries were prepared from 2 μg of total RNA using TruSeqTM RNA sample preparation kit v2 as per the manufacturer’s low-throughput protocol (Illumina).

treatment_protocol: Knockdown (see column under samples): Cells at 40-50% confluence were transfected with negative control or EHF siRNA using RNAiMax Lipofectamine 2000 reagent at a final concentration of 30 nM.  At 72h post transfection, the cells were washed in PBS and immediately harvested for RNA extraction using TRIzol® (Life Technologies). Overexpression: A549 stable clones overexpressing EHF from pcDNA3.1-EHF or control clones carrying pcDNA3.1- empty vector were generated by Lipofectin (Life technologies) transfection, followed by G418 selection. Clones were seeded in 6 well plates and when confluent, the cells were washed in PBS and immediately harvested for RNA extraction using TRIzol® (Life Technologies).

value: lung carcinoma

tag: treatment- reagent

value: pcDNA3.1-EHF vector

tag: treatment- knockdown v. overexpression

value: overexpression


title: A549 EHF-overexpressing clone 30 rep 5


title: adipocytes_H3K9me3

city: Boston

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

data_processing:
ChIP-seq reads were aligned to mouse genome (mm9) using MAQ
Duplicated reads were removed using Samtools.
Reads were sorted by Samtools
peaks were called using in-home made algorihtm..
peaks of same epitopes from different treatments were merged.
Genome_build: mm9
Supplementary_files_format_and_content: text file containing information of peaks called.

growth_protocol: Cells from the stromal-vascular fraction (SVF) were plated in culture and differentiated as described .

extract_protocol:
The chromatin was then fragmented to a size range of ~200 to 600 bp using a Branson 250 digital sonifier (sonication conditions were separately optimized for each sample). Solubilized chromatin was then diluted and incubated with  1-2 ug antibody overnight at 4°C. Immune complexes were captured with ~ 0.02 ml protein A-sepharose, washed and eluted. Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65°C, phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. Isolated ChIP DNA was resuspended in RNAase treated water and quantified using the Qubit assay (Invitrogen).
ChIP assays were performed using the following antibodies: H3K4me1 (Abcam ab8895, lot 38311/659352, H3K4me3 (Milipore 07-473, lot DAM1623866), H3K27ac (Active Motif 39133, lot 31610003), H3K36me3 (Abcam ab9050, lot 499302, H3K27me3 (Millipore 07-449, lot DAM1514011), H3K79me2 (Cell Signaling 9757, lot 1).

treatment_protocol: Murine 3T3-L1 adipocytes were treated separately with dexamethasone (Dex; 20nM) or tumor necrosis factor-alpha. To comprehensively assess epigenomic changes caused by Dex and TNF in a time-dependent manner, we profiled cells at early (2 hours), intermediate (24 hours), and late (6 days) points in the development of insulin resistance.

tag: chip antiboy

value: control


title: H3K27me3 marks of naïve LIS2 ES stem cells

value: ICM-derived LIS2


title: A549 EHF-overexpressing clone 30 rep 1


title: A549 EHF-overexpressing clone 23 rep 5


title: adipocytes_H3K4me3


title: adipocytes_H3K4me1


title: A549 EHF-overexpressing clone 23 rep 4


title: A549 EHF-overexpressing clone 23 rep 3


title: adipocytes_H3K36me3


title: adipocytes_H3K27me3


title: A549 EHF-overexpressing clone 23 rep 2


title: TNF6D_WCE

value: WCE

value: TNF


title: TNF6D_H4K20me1


title: adipocytes_H3K27ac


title: TNF6D_H3K9me3


title: TNF6D_H3K79me2


title: TNF6D_H3K4me3


title: TNF6D_H3K4me1


title: A549 EHF-overexpressing clone 22 rep 5


title: adipocytes_H4K20me1


title: adipocytes_WCE


title: A549 EHF-overexpressing clone 22 rep 2


title: TNF6D_H3K36me3


title: A549 EHF-overexpressing clone 22 rep 1


title: TNF6D_H3K27me3


title: A549 EHF-overexpressing clone 22 rep 4


title: TNF6D_H3K27ac


title: A549 EHF-overexpressing clone 30 rep 2


title: adipocytes_H3K79me2


title: A549 negative control clone 10 rep 5

source_name: lung carcinoma cells_overexpression_control empty vector

value: pcDNA3.1- empty vector


title: A549 negative control clone 10 rep 4


title: TNF2H_H3K9me3


title: TNF2H_H3K79me2


title: TNF2H_H4K20me1


title: TNF2H_H3K4me3


title: Sample_393

city: Burlington

first: David

middle: E

last: Kerr

state: VT

address: 500 Main Street 205 Terrill Hall

department: Animal Science

institute: University of Vermont

description: gDNA enriched for regions with methylated CpG sites by protein pulldown.

data_processing:
Library strategy: MIRA-Seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the UMD v. 3.1 bovine genome. Only reads with a median q score above 20 were considered for mapping.
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Tab-delimited text files include raw reads mapping to genomic location.

organism: Bos taurus

source_name: Bovine dermal fibroblasts, 16 months old

growth_protocol: Fibroblasts were grown in DMEM supplemented with 5% fetal bovine serum, 1X ITS, and 1X Penn/Strep antibiotic in a T75 flask.

extract_protocol:
gDNA was collected using the ArchivePure DNA extraction kit (5 Prime, Gaithersburg, MD).
Libraries were constructed based upon manufacturer's instructions for the Active Motif MethylCollector Ultra-seq kit. Briefly, genomic DNA was fragmented by sonication, repaired and ligated with Illumina sequencing adapters. Enrichment for methylated DNA was conducted using the kit's provided nickel-coated dual protein (methyl-binding domain proteins) pulldown. Sequencing of the enriched library was then conducted following recommendations from Illumina.

treatment_protocol: No treatment was imposed on the cells.

tag: breed

value: Holstein

tag: animal age at sampling

value: 16 months

value: dermal fibroblasts

tag: passage

tag: animal #


title: A549 negative control clone 10 rep 3


title: Sample_391

source_name: Bovine dermal fibroblasts, 5 months old

value: 5 months


title: TNF2H_H3K4me1_repeat_2

tag: treatment

tag: time


title: Sample_373

tag: cell type


title: TNF2H_WCE

tag: cell line


title: A549 negative control clone 5 rep 4


title: A549 negative control clone 10 rep 2


title: TNF2H_H3K4me1_repeat_1


title: Sample_371


title: A549 negative control clone 5 rep 2


title: TNF2H_H3K36me3_repeat_2


title: Sample_321


title: TNF2H_H3K27me3_repeat_1


title: Concat_938

description: mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the UMD v. 3.1 bovine genome. Only reads with a median q score above 20 were considered for mapping.
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Tab-delimited text files include raw reads mapping to genomic location.

source_name: Bovine dermal fibroblasts, 16 months old, 8 hrs post LPS

growth_protocol: Fibroblasts were grown in DMEM supplemented with 5% fetal bovine serum, 1X ITS, and 1X Penn/Strep antibiotic in a T75 flask and then challenged in two wells of a 6-well plate. Cell lysates from the two wells were pooled prior to RNA isolation.

extract_protocol:
mRNA collected following treatment using the 5 Prime RNA PerfectPure Extraction Kit.
Massively Parallel sequencing library preparation was performed in accordance to the Illumina TruSeq RNA Sample Prep LT version 2 (RS-122-2001/2002). Briefly, each sample was Poly-A enriched for mRNA followed by reverse transcription step with SuperScript II (Invitrogen) to convert mRNA to cDNA. Fragmentation, end repaired and adenylated followed by ligation with Illumina indexed adaptors. Each adaptor contains a universal PCR primer and flow cell binding site. Each index sequence is unique for the purpose of labelling each sample with its own unique sequence for individualization and demultiplexing purposes. PCR enrichment/amplification is performed using an Illumina specific PCR master mix for a predetermined number of PCR cycles. PCR cycles are predetermined using a standard PCR cycle titration in order to keep the number of cycles to a minimum and reduce the potential for duplicate sequences in the final data. Generally, 6-10 cycles are required. The enriched PCR product is cleaned using Ampure Beads (Beckman Coulter) and the resulting product is quantified using a Qubit Spectrofluorometer and Agilent Bioanalyzer 2100 High sensitivity DNA chip.

treatment_protocol: Cells were exposed to 100ng/ml of LPS (Sigma, St. Louis, MO).

value: lipopolysaccharide (LPS)

tag: hours post lps


title: A549 negative control clone 5 rep 1


title: Concat_932

description: mRNA

source_name: Bovine dermal fibroblasts, 16 months old, 2 hrs post LPS


title: TNF2H_H3K36me3_repeat_1


title: A549 negative control clone 1 rep 1


title: TNF24H_WCE


title: TNF24H_H4K20me1


title: TNF2H_H3K27me3_repeat_2


title: Concat_930

description: mRNA

source_name: Bovine dermal fibroblasts, 16 months old, 0 hrs post LPS


title: Calu-3 EHF siRNA rep5

value: lung adenocarcinoma

value: Silencer select EHF siRNA (s25399, Ambion)

value: knockdown


title: A549 negative control clone 1 rep 2


title: Sample_323


title: TNF2H_H3K27ac


title: TNF24H_H3K9me3


title: Calu-3 EHF siRNA rep3


title: TNF24H_H3K79me2


title: A549 negative control clone 1 rep 3


title: A549 negative control clone 5 rep 3


title: Calu-3 EHF siRNA rep4


title: Concat_738

description: mRNA


title: Concat_912

description: mRNA

source_name: Bovine dermal fibroblasts, 5 months old, 2 hrs post LPS


title: Concat_732

description: mRNA


title: Calu-3 EHF siRNA rep2


title: TNF24H_H3K4me3


title: TNF24H_H3K4me1


title: Concat_730

description: mRNA


title: TNF24H_H3K27me3


title: Calu-3 EHF siRNA rep1


title: Concat_918

description: mRNA

source_name: Bovine dermal fibroblasts, 5 months old, 8 hrs post LPS


title: TNF24H_H3K36me3


title: Concat_718

description: mRNA


title: Calu-3 negative control siRNA rep 4

value: Silencer select negative control siRNA #2 (Ambion)


title: Calu-3 negative control siRNA rep 5


title: Concat_712

description: mRNA


title: TNF24H_H3K27ac


title: Concat_910

description: mRNA

source_name: Bovine dermal fibroblasts, 5 months old, 0 hrs post LPS


title: Concat_710

description: mRNA


title: Concat_238

description: mRNA


title: Dex6D_WCE

value: Dex


title: Dex6D_H4K20me1


title: Calu-3 negative control siRNA rep 1


title: Dex6D_H3K79me2


title: Concat_218

description: mRNA


title: D1T14C

description:
Differentiation 1, 80% confluency
D1_UMI.dat

tag: starting material

value: single cells

tag: differentiation

value: Differentiation 1, 80% confluency

tag: sorting#

value: Hoechst only

tag: scrb-seq variant#

value: SmartScribe

tag: time point

value: Day 14


title: Concat_230

description: mRNA


title: D1T14B


title: Concat_212

description: mRNA


title: Dex6D_H3K9me3


title: Dex6D_H3K4me3


title: Calu-3 negative control siRNA rep 3

tag: treatment- reagent


title: D1T9C

value: Day 9


title: Dex6D_H3K27me3


title: Concat_210

description: mRNA


title: D1T9A


title: D1T7B

value: Day 7


title: Dex6D_H3K36me3


title: D1T7C


title: Calu-3 negative control siRNA rep 2

tag: treatment- knockdown v. overexpression


title: Dex6D_H3K27ac

tag: chip antiboy


title: D1T7A


title: D1T5D

value: Day 5


title: Dex2H_H3K9me3


title: D1T5C


title: Concat_232

description: mRNA

tag: breed

value: Holstein

value: 16 months


title: Dex2H_H3K79me2


title: Dex2H_H4K20me1


title: D1T14A


title: Dex6D_H3K4me1


title: D1T3D

value: Day 3


title: Dex2H_H3K4me3


title: Dex2H_WCE

value: WCE


title: Dex2H_H3K4me1


title: Dex2H_H3K27me3


title: D1T3B


title: D1T2D

value: Day 2


title: Dex2H_H3K36me3


title: D1T5A


title: Dex24H_WCE


title: D1T1C

value: Day 1


title: Dex24H_H4K20me1


title: Dex24H_H3K79me2


title: D1T2B


title: D1T2C


title: D1T1B


title: Dex24H_H3K9me3


title: Dex24H_H3K4me3


title: D1T0C

value: Day 0


title: D1T1A


title: D1T0B


title: D1T3C


title: Dex24H_H3K36me3


title: D1T0A


title: Dex24H_H3K27ac


title: Dex24H_H3K27me3


title: PBS RNA-Seq

city: Pittsburgh

first: Kyle

middle: J

last: Bibby

state: PA

address: 3700 O'Hara Street

department: Civil and Environmental Engineering

institute: University of Pittsburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequenced were adapter trimmed. The resulting files were then trimmed for low quality scores (q30) and length (<70 nt discarded)
RNAseq analysis in CLC Genomics Workbench v6.5.1 was conducted by adding both R1 (Forward) and R2 (Reverse) reads for each sample and obtaining single output files for Flowback exposed and PBS exposed treatments. The data was normalized using count based normalization method in CLC Genomics Workbench.
Kal's Z test statistic was calculated by setting up experiment in the CLC Genomics Workbench.
FDR was calculated and genes with FDR corrected Kal's Z p ≤ 0.05 were considered significant.
Genome_build: NC_012660
Supplementary_files_format_and_content: The files are tab delinited text files and contain RPKM values for features.

organism: Pseudomonas fluorescens

source_name: Exposed to PBS for one hour

growth_protocol: The P. fluorescens was maintained on cetrimide agar plates. Overnight broth cultures of P. fluorescens were diluted 100 fold in fresh LB broth and incubated at 25°C, 200 rpm and grown to OD600 ≈0.3.

extract_protocol:
Following exposure, the cells were collected by centrifugation at 2500 x g and RNA was extracted using Trizol according to manufacturer's instruction. RNA was extracted from three independent experiments conducted on different days and pooled before library construction. A total of 1 µg RNA was processed through the ScriptSeq-Complete kit Bacteria (Cat # BB1206)  library construction kit.
RNA libraries were prepared using ScriptSeq Complete Kit for Bacteria (Epicenter, Madison, WI).

treatment_protocol: The cells were collected from 10 ml overnight cultures by centrifugation at 2000 rpm. The cells were resuspended in one ml flowback water or PBS.

tag: genotype

value: Wild type


title: FW RNA-Seq

source_name: Exposed to flowback water for one hour


title: TET3 Deletion Zygotes

status: Public on Dec 22 2014

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on an HiSeq2000 using the default RTA (v1.9) analysis software.
Raw Bisulfite-Seq reads were pooled and trimmed to remove both poor quality calls and adapters using Trim Galore (v0.3.5, default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.10.0 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults.
Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 4bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.10.0) with the following parameters: a) paired-end mode: --no_overlap --report --ignore 4 --ignore_r2 4; b) single-end mode: --report --ignore 4.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Zygote

growth_protocol: Mice with a conditional deletion in the Tet3 gene were generated for a previous study (Santos et al., Epigenetics Chromatin 2013, 6:39). Briefly, C57BL/6NTac ES cells (TaconicArtemis) were targeted with a vector introducing LoxP sites around exon five of Tet3 RefSeq NM_183138.2 (sequence: CCGGACCTGTGCTTGCCAAGGCAAAGACCCTAACACCTGCGGTGCCTCCTTCTCCTTCGGCTGTTCCTGGAGCATGTACTTCAACGGCTGCAAATATGCTCGGAGCAAGACGCCACGAAAGTTCCGCCTCACGGGAGACAATCCGAAGGAG) which encodes residues required for chelation of Fe(II) and is upstream of exons containing other key catalytic residues. Expression of Cre recombinase results in excision of this region and a frame-shift from exon six affecting all downstream exons until a premature stop codon in exon seven. Animals heterozygous for the floxed allele were bred to a transgenic mouse line containing Zp3-Cre on a C57BL/6J  background and homozygous floxed mice were generated by inter-crossing to give either control females (flox/flox, Zp3-) or conditional deletion (referred to as ‘TET3’) females (flox/flox, Zp3+). Complete efficacy of Cre excision was confirmed in the oocytes of conditional deletion females by RT-PCR between exons four and six followed by Sanger sequencing. Our previous study confirmed that TET3 activity is abolished in zygotes derived from flox/flox Zp3+ females.

extract_protocol:
Frozen zygotes were lysed by incubation in a 1% SDS solution containing 0.2 µg/µL Proteinase K (Sigma) for one hour at 37ºC.
Bisulfite conversion was performed directly on the lysate using the Imprint DNA Modification kit (Sigma) according to the manufacturer’s 2-step protocol, with the modification that samples were incubated at 65ºC for 90min, 95ºC for 3min then 65ºC for 20min. After addition of 1 µg yeast carrier RNA (Qiagen), treated DNA was purified with the PureLink PCR Micro Kit (Invitrogen) according to the manufacturer’s instructions. Before elution of DNA, on-column desulfonation was performed by incubation with BD buffer (Qiagen) for 8min. A complementary strand was synthesised by combining 1X NEB2 buffer (NEB), 0.25 mM dNTP mix (Roche) and 0.8 µM biotin labelled random tetramer primer (biotin-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNN) with purified DNA. This mix was incubated at 65ºC for 5min then 4ºC for 5min, followed by addition of 1 U/µL Klenow 3’-5’ exo- (NEB) and incubation at 4ºC for 15min. The temperature was then raised to 37ºC by 1ºC/min, and samples were incubated at 37ºC for 90min. DNA was purified using a 1:1 ratio of AMPure XP beads (Agencourt) according to the supplier’s protocol. The biotin-labelled strand was captured with Dynabeads M280 Streptavidin beads (Invitrogen) by incubation at RT for 20min, then separated from the original bisulfite treated strand by denaturation with freshly prepared 0.1N NaOH. While still on the beads, DNA complementary to the biotin-labelled strand was synthesised in the same manner as described above but with a non-labelled random tetramer primer (CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNN). The beads were resuspended in a mixture of 1X ThermoPol Reaction Buffer (NEB), 0.25 mM dNTP mix and 0.16 U/µL Bst DNA Polymerase Large Fragment then incubated at 65ºC for 30min. To elute from the beads, DNA was resuspended in a reaction mix composed of 1X Phusion HF Buffer (NEB), 0.25 mM dNTP mix, 0.4 µM PE1.0 oligo (Illumina) and 0.04 U/µL Phusion High-Fidelity DNA Polymerase (NEB) then incubated at 94ºC for 5min, 55ºC for 10min and 72ºC for 30min. DNA was purified using a 1:1 ratio of AMPure XP beads (Agencourt) according to the supplier’s protocol. PCR amplification was performed to generate a suitable library concentration for sequencing. The PCR reaction mix was composed of 1X Phusion HF Buffer (NEB), 0.1 mM dNTP mix, 0.4 µM each PE1.0 and PE2.0 oligos (Illumina) and 0.02 U/µL Phusion High-Fidelity DNA Polymerase (NEB). Cycling was performed by initial denaturation at 98ºC for 30s, followed by cycles of 98ºC for 20s, 65ºC for 20s and 72ºC for 20s, then a final extension at 72ºC for 5min.

treatment_protocol: Female mice were superovulated by intraperitoneal injection of pregnant mare’s serum followed by intraperitoneal injection of human chorionic gonadotrophin (hCG) 48 hours later. Superovulated females were naturally mated with a stud from a 129S2/SvHsd or C57BL/6J background and examined for a vaginal plug the following day. Zygotes were collected 12-13 hours after the presumed time of insemination (i.e. 24-25 hours post-hCG injection), at which stage zygotes have completed S-phase. Verification of pronuclear stage in batches of zygotes was performed manually.

tag: developmental stage

value: Post-replicative zygote

tag: strain

value: Maternal:C57BL/6J background; Paternal:129S2/SvHsd or C57BL/6J

tag: genotype/variation

value: TET3 Deletion


title: Dex24H_H3K4me1

tag: treatment

value: Dex

tag: time


title: Control Zygotes

value: Control


title: WT1_RNA-seq

city: Sherbrooke

first: Louis-Charles

last: Fortier

state: Quebec

address: 3201 Jean Mignault

department: Microbiology and Infectiology

country: Canada

institute: Université de Sherbrooke / FMSS

data_processing:
Sequencing runs were processed with Illumina CASAVA 1.8 software
The overall quality of raw sequencing data was verified with the FastQC program v10.1
Alignments were performed with Bowtie2 version 2.1.0 with default (--end-to-end) alignment mode and by specifying --sensitive as additional parameter.
uniquely mapping reads were extracted from SAM files by filtering for the 'XS:' tag
uniquely-mapped reads were sorted with htseq-count command from HTSeq package version 0.5.4 with the following parameters: -m intersection-nonempty -s no -t gene -i locus_tag
RPKM values were calculated according to Mortazavi et al., Nat Methods. 2008
Differential expression analysis and statistical comparison between wild type and lysogen transcriptomes was performed with DESeq2
Genome_build: NCBI RefSeq: NC_013316.1 and NC_015568.1
Supplementary_files_format_and_content: Processed data are presented in tab-delimited text files and include RPKM values for each sample

organism: Clostridioides difficile

source_name: bacterial RNA

growth_protocol: 12 hours growth in TY broth

extract_protocol:
Bacterial cells were harvested by centrifugation, resuspended in TRIzol reagent (Life Technologies, Cat. No. 15596-026) and mechanically lysed with glass beads on Fast Prep  aparatus. Total RNA from TRIzol was extracted with chloroform and precipitated with isopropanol.
4 μg of total RNA were treated with Ribo-Zero™ rRNA Removal Kit for Gram-Positive Bacteria (Epicentre Biotechnologies). Residual RNA was cleaned up using RiboMinus™ Concentration Module columns (Invitrogen) and eluted directly in the Elute/Frag/Prime buffer of the Illumina TruSeq RNA Sample Preparation Kit v2. The remaining of the protocol has been performed as per the manufacturer’s recommendation, except that cDNA was sheared on a Covaris instrument. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (D-Mark). Average size fragment was determined using a 2100 Bioanalyzer (Agilent Technologies) instrument. cDNA libraries were multiplexed on a single sequencing lane and sequenced on a HiSeq2000 system using 9 pM as estimated by qPCR (Kapa Biosystems) for 50 cycles yielding single-end 50 nucleotide reads. Fastq files were generated using HCS v1.5 and BclToFastq.

treatment_protocol: RNA stabilized directly in culture prior to extraction with 50:50 ethanol-aceton ice-cold solution.

value: R20291 wild type

value: ribotype 027


title: LYS2_RNA-seq

value: R20291/φCD38-2 lysogen


title: siH19 Replicate 1 (siH19_d1_myotubes)

city: Zurich

first: Jochen

last: Imig

address: Vladimir-Prelog-Weg 1-5/10

country: Switzerland

institute: ETH Zurich

data_processing:
Illumina sequencing data sets were uploaded to our ClipZ server (www.clipz.unibas.ch, Khorshid et al. Nucleic Acids Res 2011) for mapping and annotation.
The total abundance of all transcripts was normalized to 1 million in each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Table of abundance levels of RNAs after siH19 transfection and in control.

source_name: primary human myoblast

growth_protocol: primary human myoblasts from healthy donors were induced to differentiate in appropriate media

extract_protocol:
Trizol 24h post-transfection
according to Kishore et al., Nat Meth, 2011
single end reads, 5´-3´adapter, multiplexed barcoded

treatment_protocol: reverse transfection of siH19

tag: cell type

value: primary human myoblast

tag: transfection


title: siH19 Replicate 2 (siH19_d1_myotubes)


title: LYS1_RNA-seq


title: Dex2H_H3K27ac

tag: cell line


title: RNA-7 transfection Replicate 2 (miR-106a_transfections_Hela)

data_processing:
Illumina sequencing data sets were uploaded to our ClipZ server (www.clipz.unibas.ch, Khorshid et al. Nucleic Acids Res 2011) for mapping and annotation.
The total abundance of all transcripts was normalized to 1 million in each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Table of abundances of RNAs after RNA-7 transfection, after pre-miR-106a transfection, and in control.

source_name: HeLa

growth_protocol: conventional HeLa growth protocol

treatment_protocol: reverse transfection

value: HeLa


title: control transfection Replicate 2 (miR-106a_transfections_Hela)

value: control


title: pre-miR-106a transfection Replicate 2 (miR-106a_transfections_Hela)


title: RNA-7 transfection Replicate 1 (miR-106a_transfections_Hela)


title: miR-CLIP Replicate 1 (let-7g_miR-CLIP)

data_processing:
Library strategy: miR-CLIP
Illumina sequencing data sets were uploaded to our ClipZ server (www.clipz.unibas.ch, Khorshid et al. Nucleic Acids Res 2011) for mapping and annotation.
The total abundance of all transcripts was normalized to 1 million in each sample.
The abundance level of each transcript was then averaged between the two replicate samples.
Genome_build: hg19
Supplementary_files_format_and_content: Table of abundance levels of RNAs in HeLa cells (input), associated with Ago-2 (Mock), associated with Ago-2 after transfection of the let-7g capture probe RNA-12 (Ago2 IP), and captured by the let-7g capture probe RNA-12 (miRCLIP) averaged over two replicates.

extract_protocol:
Ago2 immunoprecipitation, streptavidin affinity isolation
according to Kishore et al., Nat Meth, 2011
single end reads, 5´-3´adapter, multiplexed barcoded

treatment_protocol: reverse transfection of RNA-12


title: control Replicate 1 (siH19_d1_myotubes)


title: pre-miR-106a transfection Replicate 1 (miR-106a_transfections_Hela)


title: miR-CLIP Replicate 2 (let-7g_miR-CLIP)


title: control transfection Replicate 1 (miR-106a_transfections_Hela)


title: Ago2-IP Replicate 1 (let-7g_miR-CLIP)


title: Ago2-IP Replicate 2 (let-7g_miR-CLIP)


title: Mock Replicate 1 (let-7g_miR-CLIP)


title: Mock Replicate 2 (let-7g_miR-CLIP)


title: miR-CLIP Replicate 1 (miR-106a_miR-CLIP)

data_processing:
Library strategy: miR-CLIP
Illumina sequencing data sets were uploaded to our ClipZ server (www.clipz.unibas.ch, Khorshid et al. Nucleic Acids Res 2011) for mapping and annotation.
The total abundance of all transcripts was normalized to 1 million in each sample.
The abundance level of each transcript was then averaged between the two replicate samples.
Genome_build: hg19
Supplementary_files_format_and_content: Table of abundance levels of RNAs in HeLa cells (input), associated with Ago-2 (Mock), associated with Ago-2 after transfection of the miR-106a capture probe RNA-7 (Ago2 IP), and captured by the miR-106a capture probe RNA-7 (miRCLIP) averaged over two replicates.

treatment_protocol: reverse transfection of RNA-7


title: Ago2-IP Replicate 1 (miR-106a_miR-CLIP)


title: Input Replicate 2 (let-7g_miR-CLIP)


title: miR-CLIP Replicate 2 (miR-106a_miR-CLIP)


title: Input Replicate 1 (let-7g_miR-CLIP)


title: WT2_RNA-seq


title: Ago2-IP Replicate 2 (miR-106a_miR-CLIP)


title: Input Replicate 2 (miR-106a_miR-CLIP)


title: control Replicate 2 (siH19_d1_myotubes)


title: Input Replicate 1 (miR-106a_miR-CLIP)


title: Mock Replicate 2 (miR-106a_miR-CLIP)


title: 5hmC_E14_PvuSealSeq_bio2_rep2

city: Ipswich

first: Shengxi

last: Guan

address: 240 County Road

institute: New England Biolabs

description:
5hmC biological replicate #2, technical replicate #2
E14_PvuSealSeq_b1_common_5hmC.txt

data_processing:
Basecalls performed using CASAVA Bcl2fastq
Raw sequencing reads were trimmed for adaptor sequences and low quality bases using Cutadapt
trimmed reads were mapped to the reference genome (UCSC mm9) using the Bowtie aligner with the following  parameters: - n 1 - l 25 --best --strata -m 1. Only uniquely mapped reads were kept for downstream analysis
enzyme cleavage sites were determined by the start positions of the alignments.The cytosines that are on the opposite strand 11 or 12 nucleotides downstream of enzyme cleavage sites were called 5-hydroxymethylcytosines or 5-formylcytosines.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing genomic position (bed-format), seqeunce context, strand information and sequencing counts (last column) of the common 5hmC or 5fC sites of the 2 technical replicates.

source_name: embryonic stem cell (E14)

growth_protocol: ES cells were cultured with GMEM (Invitrogen) media containing 10% FBS (Gemcell), 1% non-essential amino acids (NEAA) (Hyclone), 1% sodium pyruvate (Invitrogen), 50 μm β-mercaptoethanol (Sigma), and 1× LIF (Millipore). To maintain the undifferentiated ES cells, they were grown on 0.1% gelatin (Stem Cell Technologies)-coated culture dishes.

extract_protocol:
Genomic DNA was extracted with a Qiagen DNeasy Blood and Tissue Kit (Qiagen, Venlo, Limburg).
To generate 5hmC library, 2µg of genomic DNA was digested with ~0.7 µg of PvuRts1I at room temperature for 2 hours. Next, 30 units of T4 Phage β-glucosyltransferase (New England Biolabs, Ipswich, MA) and 75µM UDP-6N3-Glc were added to the reaction and incubated at 37 oC for 2 hours. DNA ends created by PvuRts1I were ligated with 7µM Adapter P1 (top: ACACTCTTTCCCTACACGACGCTCTTCCGATCTNN and bottom: AGATCGGAAGAG CGTCGTGTAGGGAAAGAGTGT) with T4 DNA ligase (New England Biolabs) at 16 oC overnight. The next day, genomic DNA was sheared to around 200 bp by the Covaris s-series sonicator according to the suggested settings. The sheared genomic DNA was then purified with DNA Clean and Concentrator kit (Zymo, Irvine, CA). The purified DNA was reacted with 1 mM dibenzocyclooctyne-S-S-PEG3-biotin conjugate (Click Chemistry Tools, Scottsdale, AZ) at 37 °C for 2 hours. The DNA was then purified again with DNA Clean and Concentrator kit (Zymo). Subsequently, streptavidin beads (New England Biolabs) were added to the DNA and rotated at room temperature for 2 hours. The DNA captured on the beads was washed twice with 5mM Tris pH=8.0 and 1M NaCl. After that, the DNA was end repaired and dA-tailed with NEBNext® End Repair and NEBNext® dA-Tailing Module (New England Biolabs), respectively. Subsequently, 1µM adapter P2 (top: /5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC and bottom: GACTGGAGTTCAGACGTGTGCTCTTCCGATCT) was added to perform ligation with NEBNext® Ultra™ Ligation Module (New England Biolabs) at 20 °C for 15 minutes. Lastly, 100mM DTT was added to the reaction to cleave the disulfide bond in order to release the 5hmC library from the streptavidin beads. The 5hmC library was then amplified with NEB universal and index1 primer (New England Biolabs). The library DNA was purified via Ampure Beads (Beckman Coulter, Indianapolis, IN) with the ratio 1:1 and subject to next generation sequencing pipeline.For 5fC library construction, to ensure the complete conversion of 5hmC to 5gmC, 12 µg of E14 genomic DNA were first incubated with 180 units of T4-BGT and 450µM UDP-Glc at 37oC for 3 hours. Then fresh 180 units of T4-BGT and 450µM UDP-Glc were added to the reaction at 37oC for overnight. The next day, additional 180 units of T4-BGT and 450µM UDP-Glc were added to the reaction at 37oC for 3 hours. The genomic DNA was then purified via phenol chloroform extraction.  Subsequently, 100mM of NaBH4 was added to the DNA and incubated for 2 hours at room temperature. Genomic DNA was then precipitated by ethanol and ready for library construction.

tag: passages

tag: sample type

value: Pvu-Seal-seq

value: ES


title: 5hmC_E14_PvuSealSeq_bio2_rep1

description:
5hmC biological replicate #2, technical replicate #1
E14_PvuSealSeq_b1_common_5hmC.txt


title: 5hmC_E14_PvuSealSeq_bio1_rep2

description:
5hmC biological replicate #1, technical replicate #2
E14_PvuSealSeq_b1_common_5hmC.txt


title: 5hmC_E14_PvuSealSeq_bio1_rep1

description:
5hmC biological replicate #1, technical replicate #1
E14_PvuSealSeq_b1_common_5hmC.txt


title: c8b2

status: Public on Dec 20 2014

city: Richmond

first: Karolina

middle: A

last: Aberg

state: VA

address: 1112 East Clay Street

department: Center for Biomarker Resarch & Personalized Medicine

institute: Virginia Commonwealth University

description: For each of the 19 autosomal chromosomes the described files are available for each sample in a tar archive.

data_processing:
The sequenced reads were aligned using BioScope 1.2 (Life Technologies)
We followed a previously developed an analysis pipeline for MBD-seq that includes rigorous quality control for methylome-wide investigations. Aberg KA, McClay JL, Nerella S, Xie LY, Clark SL, et al. (2012) MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case-control samples. Epigenomics 4: 605-621.
Coverage estimates were generated using a previusly described approach.van den Oord EJ, Bukszar J, Rudolf G, Nerella S, McClay JL, et al. (2013) Estimation of CpG coverage in whole methylome next-generation sequencing studies. BMC Bioinformatics 14: 50.
Genome_build: Mouse samples were aligned to the DBA2/J (D2) specific reference genome. Wang X, Agarwala R, Capra JA, Chen Z, Church DM, et al. (2010) High-throughtput sequenceing of the DBA/2J mouse genome. BMC Bioinformatics 11(Suppl 04): O7.
Supplementary_files_format_and_content: CpG-coverage file provided in comma delimited files (.csv), for each CpG coordinate in the reference genome the estimated coverage is given, which is a measure of the methylation status of that specific location ; nonCpG-coverage file provided in comma delimited files (.csv), for each nonCpG coordinate ( a C that is at least 400 bp away from any CpG coordinate) in the reference genome the estimated coverage is given, which is a measure of the background noise of that specific location.

source_name: DNA from striatum brain tissue

extract_protocol:
Genomic DNA was extracted using the Gentra Puregene Blood/Tissue Kit (Qiagen, Valencia, CA) following the vendor’s instructions. The DNA was fragmented into a median length of 180 base pairs using ultrasonication with the Covaris S2 instrument (Covaris, Woburn, MA, USA). The amount of starting material for each methylation enrichment reaction was 1.5 µg of DNA for both MethylMiner and MethylCap.
The methylation-enriched DNA from MethylMiner and MethylCap, respectively, was used as input materials for barcoded fragment libraries for SOLiD5500xl Wildfire deep sequencing. Each library was sequenced using single-end chemistry at 50 bp read length.

tag: tissue

value: brain

tag: brain region

value: striatum

tag: methylation enrichmant kit

value: MethylCap

tag: elution buffer salt concentration

value: Low salt

tag: elution approach

tag: double barcodes

tag: duplicate number


title: 5fC_E14_PvuSealSeq_bio1_rep2

description:
5fC technical replicate #2
E14_PvuSealSeq_b1_common_5fC.txt


title: 5fC_E14_PvuSealSeq_bio1_rep1

description:
5fC technical replicate #1
E14_PvuSealSeq_b1_common_5fC.txt


title: c26Sr2


title: c26Sr1


title: 26sr1

value: MethylMiner


title: c7sr1


title: 7sr3t

value: High salt

value: Single elution

value: two barcodes used, 7sr3bc10, 7sr3bc11


title: 26sr2


title: Mock Replicate 1 (miR-106a_miR-CLIP)


title: Col_MS_RNASeq_Rep#1

status: Public on Dec 21 2014

first: Hongwei

last: Guo

address: No.5 Yiheyuan Road

department: College of Life Sciences

description: mRNA sequencing of Col seedling grown on MS, biological repeat 1

data_processing: The original image data generated by sequencing machine were transferred into sequence data via base calling (Illumina Pipeline v1.3.1.) and were subjected to quality control (QC). Then raw reads were filtered into clean reads, TopHat (version 1.3.0) was used to align the reads to the Arabidopsis thaliana (TAIR10). The gene expression level was calculated by using RPKM method.

organism: Arabidopsis thaliana

source_name: Etiolated seedlings

growth_protocol: Surface-sterilized seeds were sown on respective medium and imbibed at 4Â°C for 3d. Plates were kept under light for 3~4h after imbibition to promote seed germination, wrapped with aluminum foil, and incubated in the dark at 22Â°C for 3d.

extract_protocol: 3-day-old etiolated seedlings of different samples were frozen and grinded in liquid nitrogen. Total RNA was extracted by RNeasy Plant Mini Kit (QIAGEN) from the samples, then the mRNA was fragmented into short fragments (about 350 bp) by the fragmentation buffer and converted into double-stranded cDNA by random hexamer-primer using the mRNA fragments as templates and buffer, dNTPs, RNase H and DNA polymerase I treatment. The double strand cDNA was purified with QiaQuick PCR extraction kit. Finally, sequencing adaptors were ligated to the fragments. The adaptor-ligated DNA fragments in right size were selected and purified by electrophoretic gel and enriched by PCR amplification(16 cycles). The PCR products were purified using PCR purification kit (Qiagen), and the insert size and DNA concentration were determined by bioanalyzer (Agilent) to get the final seq-library for sequencing.

treatment_protocol: Kynurenine treatment for Sample K1 and K3 were directly supplied to the growth medium

tag: growth stage

value: 3-d old

tag: ecotype

value: wild type

tag: growth medium

value: MS medium


title: Col_Kyn_RNASeq_Rep#1

description: mRNA sequencing of Col seedling grown on MS+Kyn, biological repeat 1

tag: genotype/variation

value: MS + 25mM Kynurenine medium


title: Col_MS_RNASeq_Rep#2

description: mRNA sequencing of Col seedling grown on MS, biological repeat 2


title: 8b1

tag: strain


title: 8B2


title: Col_Kyn_RNASeq_Rep#2

description: mRNA sequencing of Col seedling grown on MS+Kyn, biological repeat 2


title: wei8tar2_MS_RNASeq_Rep#1

description: mRNA sequencing of wei8tar2(+/-) seedling grown on MS, biological repeat 1


title: drought treated plant rep2

first: Yan

last: Long

state: China

address: Zhongguancun South street No.12

institute: Chinese Academy of Agricultural Sciences

description: Haloxylon ammodendron (C. A. Mey.)

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data were then filtered by data-processing steps to generate clean data via a process that included the removal of adapter sequences, reads in which unknown bases are greater than 10%, and low-quality sequences (in which the percentage of low-quality bases of quality value ≤ 5 is greater than 50% in a read). After the clean data was generated, transcriptome assembly was accomplished using Trinity software with min_kmer_cov set to 2 by default and all other parameters set to default values.
After the raw data of DGE library  was generated and the data-processing steps were completed, the clean reads were then mapped to the assembly transcriptome reference sequences using RSEM software. Mismatches of no more than 2 bases were allowed in the alignments. The read count for each gene was obtained from the mapping results.
Gene expression levels were calculated based on the numbers of reads mapped to the reference sequence, using the FPKM method. Differential expression analysis of two conditions was performed using the DESeq R package
Genome_build: de novo assembly transctiptome sequences
Supplementary_files_format_and_content: fasta format for assembled sequences and unigenes.
Supplementary_files_format_and_content: Trinity.fasta: assembled fasta
Supplementary_files_format_and_content: SSunigene.fasta

organism: Haloxylon ammodendron

source_name: Seedling

growth_protocol: H. ammodendron seeds were provided by the Gansu Desert Control Institute. The seeds were sowed on damp filter papers and incubated at 4℃ for 4 days before being placed at 23℃ under long-day (16 h light/8 h dark) conditions with a photosynthetic photon flux density of 150μmol m-2 s-1. The seedlings were grown in four pots (20 seedlings/pot) representing two replicates of two treatments.

extract_protocol:
Several tissues, including leaves, stems and roots, were then harvested from the drought and control samples for subsequent RNA isolation. Total RNA was extracted from the two replicates of the drought and control plants with TRIzol Reagent (Invitrogen, 15596-026) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After the seedlings grew for one month, one set of seedlings were treated with a one-week (7d) stress, and the second set of seedlings was used as a control and received no treatment. The control pots were irrigated from the bottom every day, while drought-stressed pots were not irrigated and were monitored for wilting symptoms.

tag: age

value: post germination 30 days

value: seedling

tag: genotype

value: drought treated plant


title: drought treated plant rep1

description: Haloxylon ammodendron (C. A. Mey.)


title: control plant rep2

description: Haloxylon ammodendron (C. A. Mey.)

value: control plant


title: wei8tar2_MS_RNASeq_Rep#2

institute: Peking University

description: mRNA sequencing of wei8tar2(+/-) seedling grown on MS, biological repeat 2


title: control and drought treated plant

description: Haloxylon ammodendron (C. A. Mey.)

value: control and drought treated


title: control plant rep1

description: Haloxylon ammodendron (C. A. Mey.)


title: iD7R_3

first: Laurie

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

description: isolated CMs, Miltenyi columns

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Bowtie v. 0.12.7, Tophat v1.3.2 and Cufflinks v 1.2.1 and Cuffdiff were utilized to determine the expression levels of genes (Trapnell et al., 2012), using a NCBIN37, ENSEMBL-based annotation and flags -p 4,  --segment-length 20 --segment-mismatches 1 --solexa1.3-quals --no-novel-juncs -r 200
Cufflinks was guided using the same annotation as Tophat with flags -b -u -p 4
Genome_build: mm9 (iGenome)
Supplementary_files_format_and_content: Txt file containing a table of FPKM values for each sample described in the study

source_name: 7 days post-resection myocardium, isolated CMs

extract_protocol:
Trizol
RNA was isolated using Trizol according to manufacturer’s instructions, including optional step in protocol. RNA quality was determined by Agilent Bioanalyzer. RNA-seq libraries were prepared as previously described (Wamstad et al., 2012) or using an Illumina TruSeq kit. A final round of size selection by Agencourt AMPure XP beads was performed to remove small fragments such as primers. Sequencing was run on either an Illumina GA-2 or Hi-Seq (barcoded).

tag: cell line

value: Primary tissue sample

tag: cell type

value: Cardiomyocytes

tag: background


title: iD7R_2

description: isolated CMs, Miltenyi columns


title: iD7R_1

description: isolated CMs, Miltenyi columns


title: c8b1

tag: tissue

value: brain

value: striatum

value: MethylCap


title: iD7S_3

description: isolated CMs, Miltenyi columns

source_name: 7 days post-sham surgery myocardium, isolated CMs


title: iD7S_2

description: isolated CMs, Miltenyi columns


title: Root QC cell 40

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

institute: Hebrew University

data_processing:
Reads were aligned to the Arabidopsis genome using Bowtie2
Gene calls were calculated by summing the number of reads hitting a gene, calculated with ngsutils. Genes with coverage of <200bp were discarded.
Genome_build: TAIR10
Supplementary_files_format_and_content: Log2 normalized expression calls for genes (Excel File)

source_name: Root QC cells

growth_protocol: WOX5:GFP (Col-0 background) plants were grown on plates (1xMS, 0.5% Sucrose, 0.8% Agar) and harvested at 5 DAS (Days after stratification)

extract_protocol:
Roots were treated with cell-wall digestion solution as in (Birnbaum et al., Nature Methods, 2005) and GFP positive cells were sorted using FACS directly into RT Buffer (Hashimshony et al., Cell Reports, 2012)
mRNA was converted to cDNA, amplified using in vitro transcription and library constructed according to CEL-Seq protocol (Hashimshony et al., Cell Reports, 2012)

value: 5 DAS


title: iD7S_1

description: isolated CMs, Miltenyi columns


title: Root QC cell 38


title: iP4_3

description: isolated CMs, Miltenyi columns

source_name: 4 day postnatal myocardium, isolated CMs


title: Root QC cell 36


title: iP4_2

description: isolated CMs, Miltenyi columns


title: iP4_1

description: isolated CMs, Miltenyi columns


title: Root QC cell 34


title: Root QC cell 35


title: iP0_3

description: isolated CMs, Miltenyi columns

source_name: 0 day postnatal myocardium, isolated CMs


title: iP0_2

description: isolated CMs, Miltenyi columns


title: iP0_1

description: isolated CMs, Miltenyi columns


title: Root QC cell 32


title: Root QC cell 27


title: Root QC cell 28


title: Root QC cell 29


title: Root QC cell 31


title: vD7S_1

description: ventricular myocardium

source_name: 7 days post-sham surgery ventricular myocardium


title: vD7S_2

description: ventricular myocardium


title: Root QC cell 30


title: Root QC cell 26


title: Root QC cell 39


title: vD7R_2

description: ventricular myocardium

source_name: 7 days post-resection surgery ventricular myocardium


title: Root QC cell 25


title: vD7R_1

description: ventricular myocardium


title: Root QC cell 24


title: Root QC cell 37


title: vD1R_2

description: ventricular myocardium

source_name: 1 day post-resection surgery ventricular myocardium


title: vD1S_2

description: ventricular myocardium

source_name: 1 day post-sham surgery ventricular myocardium


title: Root QC cell 23


title: vD1R_1

description: ventricular myocardium


title: vD1S_1

description: ventricular myocardium


title: Root QC cell 33


title: vAd_2

description: ventricular myocardium

source_name: Adult ventricular myocardium


title: Root QC cell 22


title: vAd_1

description: ventricular myocardium


title: vP7_1

description: ventricular myocardium

source_name: 7 day post-partum ventricular myocardium


title: vP4_2

description: ventricular myocardium

source_name: 4 day post-partum ventricular myocardium


title: Root QC cell 21


title: vP7_2

description: ventricular myocardium


title: vP0_2

description: ventricular myocardium

source_name: 0 day postnatal ventricular myocardium


title: ex72hr_2

description: isolated CMs

source_name: Explanted, dissociated adult cardiomyocytes, 72hr


title: ex72hr_1

description: isolated CMs


title: vP4_1

description: ventricular myocardium


title: ex48hr_1

description: isolated CMs

source_name: Explanted, dissociated adult cardiomyocytes, 48hr


title: Root QC cell 16


title: Root QC cell 20


title: Root QC cell 17


title: Root QC cell 19


title: vP0_1

description: ventricular myocardium


title: ex24hr_2

description: isolated CMs

source_name: Explanted, dissociated adult cardiomyocytes, 24hr


title: Root QC cell 18


title: Root QC cell 15


title: ex48hr_2

description: isolated CMs


title: ex0hr_2

description: isolated CMs

source_name: Explanted, dissociated adult cardiomyocytes, 0hr


title: ex24hr_1

description: isolated CMs


title: Root QC cell 13


title: TG 2

city: Los Angeles

first: Fan

last: Li

address: 675 Charles E Young Drive South

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Library strategy: CLIP-Seq
Basecalls performed with Illumina base calling software [Illumina Real time analysis(RTA) 1.13.48]
Adapter sequences were removed from the 3' end using cutadapt (http://journal.embnet.org/index.php/embnetjournal/article/view/200) with options '-a GTGTCAGTCACTTCCAGCG -e 0.06 -O 6 -m 12'
Reads were merged between replicates and then mapped to the mouse (mm9) transcriptome and genome using Tophat with options '--read-mismatches 1 --read-gap-length 1 --read-edit-dist 1 --max-multihits 100 --b2-very-sensitive --transcriptome-max-hits 100 –no-coverage-search --no-novel-juncs'
Peaks were called using Piranha with a window size of 200bp
Peaks were converted to mm10 coordinates using the UCSC liftOver utility
Genome_build: mm10
Supplementary_files_format_and_content: BED format

source_name: intestinal epithelial cells

extract_protocol:
Total intestinal epithelial cells from TRE-MSI2 mice treated with Dox for 24 hours were isolated as above, and wildtype intestinal crypts were isolated as above. For crosslinking, cell suspension was exposed to 2 pulses of 265nm UV light at 400mJ/cm2 in a Stratalinker (Model 2400, Stratagene). Epithelial cells were then lysed using PXL buffer (PBS, 01% SDS, 0.5% deoxycholate, 0.5% NP-40, plus protease inhibitor and RNAsin). The lysates were sequentially treated with DNaseI and RNase, and spin in ultra-microcentrifuge at 40,000g for 20 min. The supernatant was added to protein A Dynabeads (Dynal, 100.02) conjugated with MSI2 antibody (EMD Millipore 03-115) and incubated for 4 hours at 4 °C. 32P--ATP labeled 3’ RNA (RL-3) linker was ligated to the RNA fragment on beads overnight at 16°C. The beads were re-suspended in 30 ul of Novex loading buffer (without reducing agent), and separated with Novex NuPAGE 10% Bis-Tris gel and transferred to S&S BA-85 nitrocellulose membrane.  After overnight exposure, around 50 KD band was visualized and the corresponding membrane was cut to small pieces. The RNA was released by proteinase K digestion and isolated using RNA phenol and CHCl3 solution.
5’ RNA (RL-5) linker was ligated into the RNA fragments. The RNA was transcribed into complementary DNA using RT-PCR and amplified using Re-PCR with Solexa fusion primers.

tag: antibody

value: MSI2 antibody (EMD Millipore 03-115)

value: intestinal epithelial cells

tag: background strain


title: ex0hr_1

description: isolated CMs


title: TG 1


title: Root QC cell 12


title: Root QC cell 11


title: WT 2

value: WT


title: Root QC cell 10


title: Root QC cell 8


title: Root QC cell 9


title: Root QC cell 7


title: Root QC cell 6


title: Root QC cell 3


title: Root QC cell 2


title: Root QC cell 4


title: Root QC cell 14


title: GM19257

status: Public on Dec 19 2014

first: Sidney

last: Wang

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
Raw data provided are fastq files after the following processing. FASTX-Toolkit were used to clip the adaptor sequence and trim the 5' most base for each read. Reads that are shorter than 22-nt or that are mapped to rRNA, tRNA, snoRNA using bowtie were removed from the file.
Processed reads are then map to human genome (hg19) using tophat. Uniquely mapped reads are used to intersect with Ensembl gene annotation using BEDTools to get read count per gene for each individual.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file contains read count per Ensembl gene for each individual. It is organized with one individual per column and one gene per row.

source_name: lymphoblastoid cell lines derived fromHapMap Yoruba individual

growth_protocol: Cells were cultured at 37 degree Celsius and 5% CO2 in RPMI 1640 (supplemented with 2mM L-glutamine and 15% fetal bovine serum)

extract_protocol:
Ribosome footprint profiling experiments were performed using ARTseqTM Ribosome Profiling kit for mammalian cells (RPHMR12126) following vendor’s instructions. Cell lysates were prepared from flash frozen pellets of 30 to 50 million live cells by repeat pipetting in 1 ml cold lysis buffer. Sephacryl S400 spin column (GE; 27-5140-01) was used for monosome isolation. For rRNA depletion, Ribo-Zero Magnetic Kit (Epicentre; MRZH11124) was used.
Ribosome footprint cDNA libraries were PCR amplified (12 to 15 thermo-cycles) and barcoded using ScriptMiner Index PCR Primers (Epicentre; SMIP2124). Indexed libraries were pooled to sequence on an Illumina HiSeq 2500.

tag: gender

value: Female

value: Lymphoblastoid Cell Line

tag: enrichment type

value: ribosome protected fragments

tag: molecule subtype

value: cytoplasmic RNA


title: GM19238


title: GM19225


title: GM19223

value: Male


title: GM19239


title: Root QC cell 1

source_name: Root QC cells


title: GM19222


title: GM19204


title: GM19209


title: WT 1


title: GM19210


title: GM19193


title: GM19172


title: GM19190


title: GM19192


title: GM19160


title: Root QC cell 5


title: GM19159


title: GM19153


title: GM19144


title: GM19152


title: GM19143


title: GM19141


title: GM19207


title: GM19140


title: GM19201


title: GM19138


title: GM19200


title: GM19171


title: GM19137


title: GM19128


title: GM19101


title: GM19108


title: GM19116


title: GM19093


title: GM19131


title: GM19119


title: GM19102


title: GM19147


title: GM19127


title: GM19130


title: GM19092


title: GM19099


title: GM19114


title: GM19098


title: GM18870


title: GM18916


title: GM18913


title: GM18861


title: GM18858


title: GM18856


title: GM18912


title: GM18853


title: GM18852


title: GM18855


title: GM18907


title: GM18523


title: GM18522


title: GM18520


title: GM18909


title: GM18510


title: GM18508


title: GM18511


title: GM18516


title: GM18507


title: GM18519


title: GM18505


title: GM18499


title: GM18498


title: GM18486


title: GM18862


title: GM18501


title: eWAT551_day4

city: Odense

first: Qin

last: Hao

address: kanslergade 1

country: Denmark

institute: Copenhagen University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence by using cutadapt with parameters -m 15 -e 0.05, then mapped to refMrna downloaded from UCSC using bwa with parameters -n 1
The number of reads which uniquely mapped to the RefSeq transcripts were counted for each gene, then merged into one file for each tissue.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include tag counts for each sample ...

extract_protocol:
Adipose tissues were dissected, snap frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent 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: Mice were kept at thermoneutrality for 8 days acclimation before treatment. Mice were divided into 3 groups. Two groups were transferred to 4 degree for 2 and 4 days. The third group was sacrificed without cold exposure.

value: 8 weeks

value: male

value: epididymal white adipose tissue

tag: treatment

value: 4 day in cold exposure


title: eWAT548_day4


title: eWAT553_day4


title: eWAT539_day2

value: 2 day in cold exposure


title: eWAT532_day2


title: eWAT538_day2


title: eWAT518_day0

value: 0 day in cold exposure


title: eWAT517_day0


title: eWAT516_day0


title: iWAT553_day4

value: inguinal white adipose tissue


title: iWAT555_day4


title: GM18517


title: iWAT550_day4


title: iWAT551_day4


title: iWAT539_day2


title: iWAT548_day4


title: GM18504


title: iWAT538_day2


title: iWAT532_day2


title: iWAT522_day0


title: iWAT517_day0


title: iWAT516_day0


title: iBAT555_day4

value: interscapular brown adipose tissue


title: iBAT548_day4


title: GM18502


title: iBAT539_day2


title: iBAT534_day2


title: iBAT532_day2


title: iBAT535_day2


title: iBAT517_day0


title: iBAT518_day0


title: iBAT516_day0