title: DMSO H3Ac [ChIP-seq]

data_processing:
Illumina pipeline 1.4  was used for base calling
Reads were aligned to the mm9 genome using bwa 0.5.9 with default parameters
A set of peaks were generated for each ChIP vs Input using MACS 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: bed files comparing ChIP control vs treatment

source_name: DMSO H3Ac_ChIP-seq

growth_protocol: C57BL6 male mice (10-12 week old).

extract_protocol:
After the incubation, roughly chopped mouse left ventricle were fixed for 10 minutes with 1% formaldehyde. Glycine (0.125 M) solution was then added for another 10 minutes. Pellets were resuspended in SDS lysis buffer containing protease inhibitors. Then cells were sonicated to shear chromatin and ChIP was performed using indicated above antibodies and DynaMag™-2 magnet (Invitrogen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: C57BL6 male mice (10-12 week old) were injected subcutaneously twice daily at 0.6 mg/kg/day of TSA, as previously described (Chang et al. 2011).

tag: age

value: 10-12 weeks

tag: Sex

value: male

tag: injected with

value: DMSO (control)

value: Left ventricle


title: CCAT1_myc_3C_1 and 2

status: Public on Feb 22 2014

type: SRA

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

library_source: genomic

data_processing:
Basecalling using Illumina Casava1.8.2 software.
combine two technical replicates CCAT1_myc_3C_1.txt.gz and CCAT1_myc_3C_2.txt.gz for further analysis
The 3C-Seq data was analyzed as described by Stadhouders et al, Nat Protoc. 2013, 8:509-524 with Primer used in this assay:  p5-Scr-3C-seq-Myc-R:  AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGCCAATAATTCCAACAAACCCTAAAACG  p5-ASO-3C-seq-Myc-R:  AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTATGTCAAATTCCAACAAACCCTAAAACG  p7-3C-seq-Myc-F:  CAAGCAGAAGACGGCATACGAGCTGGAAACCTTGCACCTC  p5-Scr-3C-seq-CCAT1-F:  AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGCCAATCTTCTACTGATTGGCCCTAAAC  p5-ASO-3C-seq-CCAT1-F:  AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTATGTCACTTCTACTGATTGGCCCTAAAC  p7-3C-seq-CCAT1-R:  CAAGCAGAAGACGGCATACGACAGTAGTGGGTCTTAATGCTTG
generate bedgraph files and upload to UCSC for visualization to show the chromatin interaction between CCAT1-L and Myc locus

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HT29 cells were maintained accoriding to ATCCsuggested in ATCC-formulated McCoy's 5a Medium Modified 10 % FBS.

extract_protocol:
The 3C-Seq libraries were prepared from scramble knockdown (Scr) and CCAT1-L knockdown cells step by step as described by Stadhouders et al, Nat Protoc. 2013, 8:509-524. HindIII and DpnII were used as the primary and secondary restriction endonuclease.
The 3C-Seq library was prepared with Illumina TruSeq DNA samples preparation Kit V2 and then sequenced  with Illumina  HiSeq  2000.

tag: cell line

tag: cell type

value: human colorectal adenocarcinoma

tag: chromosome

value: diploid


title: TSA H3Ac [ChIP-seq]

status: Public on Feb 23 2014

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

organism: Mus musculus

source_name: TSA H3Ac_ChIP-seq

tag: strain

value: TSA (0.6 mg/kg/day)

tag: tissue

tag: chip antibody

value: Anti-acetyl-Histone H3

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: 4C_Ibtk_rep2

city: Chapel Hill

first: Rex

middle: Lee

last: Williams

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina

data_processing:
Sequences processed by CASAVA v1.8
Raw sequences were filtered for 4C-primers to identify anchor and allele of origin
Raw sequences were mapped using Bowtie v0.12.7 (-n 2 -l 100 -m 1 --best --strata)
Mapped sequences were processed using custom Perl scripts and the fourSig analysis package to identify significant interacting regions of the genome
Interacting regions were analyzed using custom R scripts to identify interacting fragments between replicate libraries and alleles
Genome_build: mm9
Supplementary_files_format_and_content: All text files are tab delimited and contain genomic coordinates for interactions and read counts.

source_name: Trophoblast Stem Cells

growth_protocol: TS cells were cultured as previously described (Calabrese et al., 2012, Quinn et al., 2006)

extract_protocol:
Genomic DNA was extracted as fixed chromatin from nuclear lysates and fragmented by restriction digest.  See methods in Williams et al., 2013
4C libraries were constructed using a modified, locus-specific protocol for 4C-Seq.  See methods in Williams et al., 2013

treatment_protocol: TS cells were removed from feeder cells and grown feeder-free for 2 passages prior to fixation.

value: F1 hybrid trophoblast stem cells derived from blastocyst

tag: passage

value: Cast/EiJ x C57BL/6


title: 4C_Ibtk_rep3


title: 4C_Ibtk_rep1


title: Ad_Front_NeuN_pos.TARRBS

city: Beijing

first: Xianlong

last: Li

address: 5, Yiheyuan Rd., Haidian District

department: Biodynamic Optical Imaging Center, College of Life Sciences

institute: Peking University

data_processing:
Base calling is performed by CASAVA_v1.8.2
Alignment is performed by Bismark v0.7.6
Convert alignment results to information of each base of reference sequence, using SAMTools mpileup v0.1.18 (r982:295)
Calculate modification p-value of each site using R (version 2.14.2) function dbinom(), then assess FDR using Benjamini-Hochberg method
Genome_build: hg19
Supplementary_files_format_and_content: hmC modification level of each site

source_name: brain

extract_protocol:
500 mg of cryopreserved human left frontal cortex was homogenized on ice by douncing in 5 ml lysis buffer (0.32 M Sucrose, 5 mM CaCl2, 3 mM, 0.1mM EDTA, 10 mM Tris-HCl (pH 8.0), 1 mM DTT, and 0.1% TritonX-100). Homogenates were transferred to ultracentrifuge tube, with Sucrose Solution (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl (pH 8.0)) carefully pipetted at the bottom of the tube to form a concentration gradient. Ultracentrifugation was performed at 100,000 g for 2.5 hrs at 4°C. After centrifuge, supernatant including debris was removed and the pellet was incubated in 0.5 ml cold PBS on ice for 20 min before thoroughly triturated by pipetting. Immunostaining mix was prepared by combining 300 µl PBS, 1.2 µg NeuN antibody (Millipore, MAB377), 200 µl Blocking Mix ( 2.5% BSA and 10% Goat Serum in PBS), and 2 µg of Alexa Fluor 488 conjugated secondary antibody (Cell Signaling, #4488) together and rotated for 5 min at room temperature in the dark. An isotype antibody control was processed in parallel by adding the same amount of mouse IgG instead of NeuN antibody. Then 1 ml nuclei suspension was added, and the mixture was incubated by rotating in the cold room for 45 min. After incubation, samples were retrieved and stained with Hoechst 33342 for another 2 min. The immunostaining result was checked under the microscope. Immumotagged samples were diluted 10 times in PBS and filtered through a 40μm filter before loaded to the FACS machine. A preliminary run was performed to gate out the proper nuclei size and the fluorescence bright population before the sort which separate the NeuN+ nuclei. Once the sort was done, a small amount of sorted sample was run again through the instrument to confirm the purity. After FACS, PBS was added to raise the volume of the sort to 10 ml. Then the sorted sample was mixed with 2 ml Sucrose Solution, 50 µl CaCl2 (1 M), and 30 µl Mg(Ac)2 (1 M), and incubated on ice for 15 min before centrifuged at 1786 g for 15 min at 4°C. The NeuN+ nuclei pellet was resuspended in PBS. DNA was extracted by Qiagen Blood & Cell Culture DNA Kits following the manufacture’s instructions.
Genomic DNA extracted from purified neuron nucleus were first digested with MspI for 3 hours at 37 °C and purified using QIAquick columns. Then, glycosylation and oxidation of the DNA was performed similar to the TAB-Seq, except for an  additional  size selection  of 180-600 bp fragments on a 2% agarose gel was performed after the adapter ligation.

value: frontal lobe

tag: developmental stage

value: adult

value: NeuN+ neurons


title: upf3Δ

status: Public on Feb 21 2014

city: Los Angeles

first: Stephen

last: Douglass

state: CA

address: 5128 TLSB Terasaki Life Sciences Building, 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Open Biosystems

library_source: transcriptomic

data_processing:
Basecalls were done by Illumina
Sequence reads were align by Novoalign allowing 4 mismatches and no gaps
Reads that failed to align were aligned using BLAT allowing 3 mismatches and gaps up to 20000 nucleotides in length
Coverage tracks were generated from alignments as wig files
Genome_build: UCSC version: sacCer2
Supplementary_files_format_and_content: wig files were generated using in-house scripts; values represent sequencing depth-normalized log10 values of sequence coverage

molecule: total RNA

organism: Saccharomyces cerevisiae BY4741

source_name: Yeast cells

growth_protocol: 25°C in YPD medium

extract_protocol:
Hot phenol RNA extaction
Constructed by Illumina using standard protocol

treatment_protocol: Untreated RNA

tag: genotype/variation

tag: growth phase

value: Exponential


title: Pop-Cytoplasm

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

description: Sample 3

data_processing:
Triming: Web-based analyzing tools: miRanalyzer version 03/2012
Read mapping to databses: bowtie via a web-based analyzing tools: miRanalyzer version 03/2012
RNA secondary structure prediction: RNAfold via a web-based analyzing tools: miRanalyzer version 03/2012
Genome_build: Aedes agypti genome "aaeSCL" in miRanalyzer web server (equivalent to AaegL2 in VectorBase); miRbase version 19.
Supplementary_files_format_and_content: Tab-delimited .txt file reports miRNA expression values

organism: Aedes aegypti

source_name: Cytoplasmic fraction of Pop cells

growth_protocol: Ae. aegypti Aag2 cells were maintained in growth media in a 1:1 mixture of Mitsuhashi–Maramorosch and Schneider’s insect media (Invitrogen) supplemented with 10% FBS.

extract_protocol:
Cytoplasmic and nuclear fractions were isolated using PARISTM kit (Ambion) according to the manufacturer’s instructions.
A small RNA library was generated from all samples using the Illumina Truseq™ Small RNA Preparation kit at LC Sciences Company (Houston, USA).

treatment_protocol: Aag2 cells infected with the wMelPop-CLA strain of Wolbachia (+Wol) were maintained as Aag2 cells.

tag: host developmental stage

value: Embryonic

tag: host cell line

value: Aag2 cells

tag: host cell fraction

value: Cytoplasm

tag: infection

value: wMelPop-CLA strain of Wolbachia


title: Aag2-Cytoplasm

description: Sample 1

source_name: Cytoplasmic fraction of Aag2 cells


title: Aag2-Nucleus

description: Sample 2

source_name: Nuclear fraction of Aag2 cells

value: Nucleus


title: upf2Δ

description: Open Biosystems


title: DR1(pAST2)-control

city: Seoul

first: Hyerim

last: Hong

address: Korea Univ. Anam Campus, Anam-dong 5-ga, Seongbuk-gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea University

description: control

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1)
Supplementary_files_format_and_content: DR1(pAST2)-control.txt

organism: Acinetobacter oleivorans DR1

extract_protocol: Total RNA was isolated from 5 ml of stationary cells, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions. The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina Genome Analyzer IIx to generate single-ended 36-bp reads.

value: Wild type harboring pAST2

value: exponential


title: Wildtype

description: Open Biosystems

value: wildtype


title: NC-3

city: Sendai

first: Toru

last: Nakazawa

address: 1-1 Seiryo

department: Ophthalmology

country: Japan

institute: Tohoku University

description: six retinas (from six mice) per sample

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using CLC genomics workbench software (version 6.0.1) (CLC Bio, Aarhus, Denmark).
Reads Per Kilobase of exon per Million (RPKM) were calculated with CLC genomics workbench software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: csv files include RPKM values for each Sample

source_name: Retina

extract_protocol:
Retinas were removed, immediately immersed in an RNA stabilization reagent, and then RNA was harvested using miRNeasy mini kit. Thirty-six samples of purified RNA (18 from the ONC and 18 from the control group) were used for this analysis. In each group, fixed quantities of RNA were taken from six samples and combined into a single sample, in order to minimize the influence of individual variations in the mice. This process yielded three combined samples from both the ONC and control groups.  Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ONC was used to induce axonal injury. The optic nerve was exposed, crushed 2 mm posterior to the globe with fine forceps for 10 seconds, and released. The operation was similar in the sham group, but after exposure, the optic nerve was not crushed.

tag: treatment

value: optic nerve crush

value: retina

tag: age

value: 12 week-old

tag: genotype

value: wild type


title: NC-2

description: six retinas (from six mice) per sample

tag: strain


title: NC-1

description: six retinas (from six mice) per sample

tag: tissue


title: Sham-2

description: six retinas (from six mice) per sample

value: sham


title: GM12004_chromatin_RNA

city: Ann Arbor

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

institute: HHMI/University of Michigan

description: chromatin-bound RNA

data_processing:
Sequence analysis-Low-quality bases as designated by Illumina were trimmed from the 3’ end of reads, and reads shorter than 35bp were removed.  The resulting reads were aligned to an index comprising the human reference genome (hg18) and the Epstein-Barr virus genome (NC_009334.1) using GSNAP (version 2012-04-10).  A list of SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.  The following parameters were used: Mismatches ≤[(read length+2)/12-2]; Mapping score ≥20;  Soft-clipping on (-trim-mismatch-score=-3);  Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted.  SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments.  Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.
Levels of transcripts were analyzed using RSeQC.  RPKM (read per kilobase per million reads) for each gene were calucated.
Genome_build: HG18
Supplementary_files_format_and_content: Text files that contain RPKM values

source_name: B-cells

growth_protocol: Cultured B-cell lines from two CEPH individuals (Centre d'Etude du Polymorphisme Humain), GM12004 and GM12750, were obtained from Coriell Cell Repositories (Camden, NJ, USA).  The B-cells were grown to a density of 5x105 cells/mL in RPMI 1640 supplemented with 15% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/L L-glutamine.  For downstream experiments, cells were harvested 24 hours after addition of fresh medium.

extract_protocol:
For chromatin-associated nascent RNA-seq, cultured B cells were treated with cell fractionation buffer from the PARIS kit (Ambion) following manufacturer’s protocol to obtain a nuclei pellet.  Chromatin fraction was extract from this pellet as previously described (Pandya-Jones and Black, RNA, 15, 1896, 2009).  Briefly, the nuclei pellet was washed with ice-cold 1× PBS containg 1 mM EDTA, then resuspended in a ice-cold glycerol buffer (20 mM Tris-HCl, pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol). An equal volume of ice-cold nuclei lysis buffer (10 mM HEPES, pH 7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M UREA, 1% NP-40) was added, the tube was gently vortexed, incubated for 2 min on ice, and then centrifuged for 2 min, 4°C at 14,000 rpm.  The supernatant was removed and the chromatin pellet was gently washed with ice-cold 1× PBS containg 1 mM.  Chromatin RNA was prepared from this pellet using TRI Reagent RT (Molecular Research Center). This RNA was further purified using the RNeasy Mini protocol (Qiagen) with on-column DNase digestion.  After being shown to be free of genomic DNA, the chromatin RNA was sequenced on HiSeq 2000 as described above.
Libraries were prepared following Illumina Directional mRNA-seq sample preparation protocol.

tag: cell type

value: B-cells

tag: individual

tag: assay

value: chromatin-associated nascent RNA-seq


title: Sham-3

description: six retinas (from six mice) per sample


title: GM12750_chromatin_RNA

description: chromatin-bound RNA


title: Pop-Nucleus

description: Sample 4

source_name: Nuclear fraction of Pop cells


title: GM12750_GROseq

data_processing:
Sequence analysis-The GRO-seq and PRO-seq samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated.  Low-quality bases as designated by Illumina were trimmed from the 3’ end of reads, and reads shorter than 35bp were removed.  The resulting reads were aligned to an index comprising the human reference genome (hg18) and the Epstein-Barr virus genome (NC_009334.1) using GSNAP (version 2012-04-10).  A list of SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.  The following parameters were used: Mismatches ≤[(read length+2)/12-2]; Mapping score ≥20;  Soft-clipping on (-trim-mismatch-score=-3);  Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted.  SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments.  Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.
RNA-DNA differences-To identify RDDs, we compared RNA sequence to its corresponding DNA sequence.  Low-quality bases (Phred quality score < 20) in both the RNA and DNA were removed from consideration.  To be included as RDD sites in the final lists, the following criteria have to be met: 1) a minimum of 10 total RNA-seq reads covering that site; 2) a minimum of 10 total DNA-seq reads covering that site; 3) DNA sequence at this site is 100% concordant, without any DNA-seq reads containing alternative alleles; 4) level of RDD (# of RNA-seq reads containing non-DNA allele/# all RNA-seq reads covering a given site) is ≥10% (a minimum of two RNA-seq reads containing RDD).  To ensure the accuracy of the RDD sites, additional filtering steps were performed using two additional mapping algorithms. First, we removed all the sites that reside in repetitive genome regions annotated by repeat masker (RepeatMasker version 3.2.7).  Second, local sequences around each RDD site were aligned to the human reference genome to rule out misalignments to paralogous sequences or remaining pseudogenes.  Specifically, for each RDD event, genomic sequences comprising sequences of length 25 bp, 50 bp, and 75 bp upstream and downstream of each site along with either the DNA variant or RNA variant were aligned to an index containing human reference genome (hg18) and sequences in hg19 but not present in hg18 using BLAT(5) (Stand-alone, v. 34x11).  The settings '-stepSize=5' and 'repMatch=2253' were used to increase sensitivity.  RDD events were removed if any of the 6 corresponding sequences aligned to another genomic location with ≤n mismatches (n=(read length + 2)/12–2) and with sequences that explain the RDD call (that is if the genomic sequences match the RNA sequence).  Lastly, to avoid potential misalignment of spliced reads in GSNAP due to its high gap penalty algorithm, we re-aligned all the RNA-seq reads that contain putative RDD alleles using BLAT (Stand-alone, v. 34x11).  Human genome sequences in hg19 that are not present in hg18 were included in our index in addition to sequences in hg18.  Here, a low gap penalty was applied during BLAT alignment in order to compensate for high gap penalty of GSNAP alignment of spliced reads.  Only RDD sites that are supported by both GSNAP and BLAT are retained for downstream analysis.
Genome_build: HG18
Supplementary_files_format_and_content: Text files that contain 1) sites and types of RNA-DNA differences; 2) FPKM values

extract_protocol: Libraries were prepared following Illumina Directional mRNA-seq sample preparation protocol.

treatment_protocol: Nuclei were isolated from B cells.  4 X 107 B cells were collected by centrifugation at 400 X g for 2 min at 4oC.  The cells were washed with 20 mL of ice-cold PBS and resuspended in 10 mL of ice-cold lysis buffer [20 mM Tris-HCl pH 7.4, 150 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 0.5% Igepal CA-630, 1X Complete Protease Inhibitor Cocktail (Roche, USA) and 4 units/mL RNAseOUT (Invitrogen, USA)].  Cell  suspension was incubated on ice for 10 minutes before nuclei were centrifuged by 500 X g for 1 min at 4oC.  Pellets containing nuclei were washed carefully with 10 mL ice-cold lysis buffer, collected by centrifugation (500 X g, 1 min, 4oC), and resuspended in ice-cold storage buffer [50 mM Tris-HCl pH 8.3, 5 mM MgCl2, 0.1 mM EDTA, 40% glycerol] to 5X106 nuclei/100 uL.  Nuclei were then snap frozen in liquid nitrogen until GRO-seq experiments.  GRO-seq and PRO-seq experiments were carried out as previously described in Core et al, Science. 2008 Dec 19;322(5909):1845-8.

value: global run-on


title: Spirodela_polyrhiza_5a

city: Shenzhen

first: Jie

last: Tang

state: Guangdong

address: Rm. E118, PKU Campus, Shenzhen University Town

institute: School of Environment and Energy, Peking University Shenzhen Graduate School

data_processing:
RTA 1.12.4.2 was used for base calling.
The raw sequences were filtered as follows: 1) poor quality reads, including reads with “N” character and reads of more than 4 bases with SQ ≤ 10 or more than 6 bases with SQ value ≤ 13; 2) reads with 5’ adaptor contaminants; 3) reads without reliable 3’ adaptor; 4) reads without the inserts; 5) reads with poly A; 6) reads shorter than 18 nt.
Genome_build: Build 4.0
Supplementary_files_format_and_content: fasta file containing ID, abundance and sequences of small RNAs

organism: Spirodela polyrhiza

source_name: whole plants, including fronds and roots

growth_protocol: S. polyrhiza were cultured in Schenk and Hildebrandt basal salt mixture liquid medium at pH 5.8 and grown in a controlled climate chamber under a photoperiod of 16h-light (100 μmol.m-2.s-1, 23°C) and 8h-dark (15°C).

extract_protocol:
Total RNA was extracted from the whole plants (fronds and roots) using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions.
Small RNAs (sRNAs) of 18-30 nt in length were first separated from the total RNA pool by size fractionation using 15% denaturing polyacrylamide gel electrophoresis. After purification, 5’ and 3’ adaptors were ligated to the sRNAs using T4 RNA ligase (Promega, Madison, WI), which were again purified and used as templates for reverse-transcription (RT) reaction. The cDNA were further purified by 15% denaturing polyacrylamide gel electrophoresis.

treatment_protocol: All the samples were immediately frozen in liquid nitrogen and stored at -80oC until further treatments.


title: MCF-7 C3

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Sample 9

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

growth_protocol: To assess the osteopontin splice variant-induced protection from cell death or cell cycle arrest through deadhesion, we plated cells on 0.4 mg/mm2 poly-HEMA for 2 days. We then harvested them for gene expression analysis by RNASeq or metabonomic analysis by NMR.

extract_protocol:
mRNA was extracted by TirReagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: tissue source

value: mammary gland

value: epithelial cells

tag: transfected with

value: osteopontin-c


title: MCF-7 C1

description: Sample 7


title: GM12004_GROseq


title: MCF-7 A2

description: Sample 5

value: osteopontin-a


title: MCF-7 A1

description: Sample 4


title: MCF-7 V3

description: Sample 3

source_name: MCF-7_vector control

value: vector control


title: MCF-7 A3

description: Sample 6


title: 60repbio2

city: Irapuato

first: Octavio

last: Martinez de la Vega

state: Guanajuato

address: km 9.6 Libramiento Norte

department: Unidad de Genómica Avanzada (Langebio)

country: Mexico

institute: Cinvestav

data_processing:
The 8 cDNA libraries  were sequenced from both  5’ and 3’ ends in a flow cell using the Illumina  MiSeq System  platform  according  to  the  manufacturer’s instructions.   We  did  three  sequencing  runs  (technical replicates)  with the aim of increase  the sequence depth.
The fluorescent image processing,  base-calling  and quality  value calculation in the three  run were performed  by the Illumina  MiSeq Control  Software,  in which 150 bp paired-end  reads were obtained
Before  assembly,  the  raw  reads  were  filtered  using  PRINSEQ 0.20.3 program  to obtain  high-quality clean reads  by removing  duplicated sequences,  the reads containing  more than  2% N rate  (the  “N ” character representing ambiguous  bases), low complexity  reads  with  entropy  less than  70 and  low-quality  reads  containing  mean quality  score Q-value ≤ 25. The Q-value is the quality  score assigned to each base by the Illumina’s base-caller from the Illumina MiSeq Control  Software, similar to the Phred  score of the base call.  The command-line  parameters for PRINSEQ 0.20.3 were:  -fastq1.fq   -fastq2.fq  -out_format3  -min_qual_mean25  -ns_max_noniupac  -derep1  -lc_methodentropy  -lc_threshold70
De  novo  assembly  of the  clean  reads  was  performed  using Trinity (release 20121005) using the DIAG (Data  Intensive  Academic  Grid facilities) with  48 G RAM per node and  using 32 Gb for the  Jellyfish step.  The  size of k-mers in Trinity is 25 by default  an the rest of the assembly parameters were used under default. The command-line  parameters used in the assembly were:  − − seqTypefq  − − left1.fq  − − right2.fq  − −CPU8  − −JM32G  − − no cleanup
RSEM version 1.2.0 was used for remapping the  reads  to  the  assembled  contigs  and  transcript quantification of the  45505 genes and 99487 isoforms assembled with Trinity.  This software estimated the expression levels taking into account read mapping  uncertainty using an Expectation-Maximization algorithm. Briefly the process consisted in run 2 steps:  first, a set of reference transcript sequences was generated  and pre-processed  by the script rsem-prepare-reference using bowtie version 0.12.7 for constructing the indexes.  The following defaults  parameters were used: rsem-prepare-reference   name_assembled_file.fasta   custom_reference_name
we filtered the genes that according to RSEM model had a sum of 0 tags in all the libraries using R.15.3 commands. The number of genes was reduced to 42,401 using this procedure.
The expression data for the 42,401 contigs in the eight sequenced libraries  was summarized  by adding  the counts  of the contigs that shared  the same identifier; i.e., we considered contigs with the same identifier to be representing the same gene. This resulted in a data  matrix  with  34,066 rows (chili  pepper  genes)  and  eight columns  (libraries).
For normalization we employed  a novel method,  based  in the  work of Good, that efficiently removes the  bias in the  fold change caused  by this  factor.
To  evaluate  differential  gene expression  (DGE)  between  neighboring  intervals, say  between  10 to  20, 20 to  40 and  40 to  60 DAA,  we used  the  facilities  within  the  R  package  edgeR.   Briefly,  for  each contrast (neighbor  interval) we entered  the  data  using the  DGEList function,  estimated common  and  tag- wise dispersion,  entered  the  corresponding   normalization factors and performed  the exact  test  via the exactTest function.
P values resulting  from the exact  test  were then  feed into the qvalue function  [17] with default  parameters, except that we set fdr.level = 0.01 to obtain  a false discovery rate  of 1%.
we used a de novo  transcriptome reference assembly with trinity  (release 20121005)
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited excell files include TPM values for each Sample

organism: Capsicum annuum

source_name: Entire fruit(pericarp,placenta and seed)

growth_protocol: Capsicum  annum  cultivar ’Serrano  Tampiqueño 74’ was germinated and  cultivated under  optimal conditions  in a completely randomized  experimental design in the greenhouse facilities. The  plants  grew in the  Summer-Spring period  and  the  flowers were tagged  imme- diately  after  anthesis.

extract_protocol:
Nucleo Spin RNA Plant (Macherey-Nagel) was used for total  RNA extraction and contaminating genomic DNA was removed  by DNase I (Macherey-Nagel) treatment during  RNA isolation  procedure  in accordance  with  the manufacturer’s protocol.
The  eight samples  (two biological  replicates  of each  state  of development; 10, 20, 40 and  60 DAA)  were prepared for RNA-seq using illumina TruSeq RNA Sample Preparation v2 Guide following manufacturer’s instructions.

treatment_protocol: The  fruits  were randomly  collected  from different plants  at  states  10, 20, 40 and  60 DAA. After  the harvest  the fruits  were cleaned with ethanol  and immediately frozen in liquid nitrogen  and stored  at  -80◦ C till use.

tag: cultivar

value: Serrano Tampiqueño 74'

tag: developmental stage

value: 60(days after anthesis)

value: Entire fruit (including seeds)


title: 60repbio1


title: MCF-7 V2

description: Sample 2


title: 20repbio1

value: 20(days after anthesis)


title: MCF-7 V1

description: Sample 1


title: 20repbio2


title: 10repbio2

value: 10(days after anthesis)


title: upf1Δ

description: Open Biosystems

tag: genotype/variation

tag: growth phase

value: Exponential


title: Sham-1

description: six retinas (from six mice) per sample

value: retina

value: 12 week-old


title: 10repbio1


title: WT_spc

status: Public on Feb 20 2014

city: Reno

first: Chong

state: Nevada

address: 1664 N.Virginia Street MS330

department: physiology

institute: University of Nevada Reno

description: wild type mouse

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm9 whole genome using Tophat2
cufflinks to assemble the transcripts
cuffdiff to analyze the differential expression
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited or ;-delimited text files include RPKM values for each Sample ...

source_name: testis pachytene

extract_protocol:
testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pachytene cell

value: 6 weeks

tag: passages

value: wild type


title: GM12004_PROseq

value: B-cells

value: precision global run-on


title: WT_rspd

description: wild type mouse

source_name: testis round sperm

value: round sperm cell


title: Stra8-KO_spc

description: The mouse testis is upf2 knockout

value: Upf2 knockout pachytene cell

value: upf2 knockout


title: Stra8-KO-3

description: The mouse testis is upf2 knockout

source_name: whole testis

value: All cell


title: Stra8-KO-2

description: The mouse testis is upf2 knockout


title: MCF-7 C2

description: Sample 8

value: mammary gland

value: epithelial cells

value: osteopontin-c


title: WT-3

description: wild type mouse


title: Stra8-KO-1

description: The mouse testis is upf2 knockout


title: WT-2

description: wild type mouse


title: WT-1

description: wild type mouse


title: sal PARP-1

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Alignemnt of ChIP-seq: CASAVA 1.8.2 aligned to mm9, and default parameters used.
Differential sites detection: diffReps 1.54, p-value cutoff 1e-4, nsd 2, method: negative binomial test.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq wig files were generated by pyicos.

source_name: Nucleus accumbens tissue

extract_protocol:
For each ChIP-seq replicate, bilateral 14-gauge NAc punches were pooled from 10 mice.
Tissue was lightly fixed to cross-link DNA with associated proteins, and the material was further sheared and immunoprecipitated using sheep anti-rabbit magnetic beads (Invitrogen) conjugated to an antibody that specifically recognizes PARP-1 (ab6079).
Immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-seq using an Illumina kit according to the manufacturer’s instructions. Each experimental condition was analyzed with independent biological triplicates. Briefly, each sample underwent end repair followed by addition of an A base to the 3′ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 2% agarose gel. The range of excision was 250–350 bp. After DNA clean up, samples were amplified with 21 cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length.

treatment_protocol: 20 mg/kg cocaine was administered through intreaperitoneal injections once daily for 7 days. Mice were sacrificed 30 minutes following the last injection of cocaine

value: Nucleus accumbens

value: SALINE

tag: antibody

value: PARP-1 (rabbit polyclonal anti-PARP, ab6079)


title: 40repbio1

value: Serrano Tampiqueño 74'

value: 40(days after anthesis)

value: Entire fruit (including seeds)


title: CC PARP-1

tag: treatment

value: chronic cocaine


title: 40repbio2


title: Th9 72h antiIL2 STAT5B

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: ChIP against STAT5B.

data_processing:
For ChIP-Seq and RNA-Seq, basecalls performed using CASAVA 1.8 (HiSeq 2000).
Raw reads were aligned to the mm8 (MGSCv36) genome assembly using Bowtie 0.12.4.
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts.
For ChIP-Seq, peaks are called using MACS 1.3.7.1; For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database.
Genome_build: MGSCv36
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.8 and unpublished python scripts, rpkm (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts.

source_name: Th9 cells, 72h, STAT5B ChIP

growth_protocol: Naïve CD4+ T cells from C57/B6 mice were cultured under Th9 condition (10 ug/ml of anti-IFNg, 40 ng/ml of IL-4, 2 ng/ml of TGF-beta, 2 ug/ml of plate-bound anti-CD3, and 1 ug/ml of anti-CD28) for the indicated time.

extract_protocol: For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols. For RNA-Seq, total RNA was extracted from 5x10^6 cells per sample using RNeasy Mini kit (QIAGEN) and the quality and concentration were determined by Nanodrop ND-1000 spectrophotometer. Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor. After repairing ends, adaptor (Illumina) was added using T4 DNA ligase (New England Biolabs), and 220-400 bp fragments were isolated using 2% E-Gel (Invitrogen) and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).

treatment_protocol: For ChIP-Seq, cells treated with Th9 condition for indicated time. For RNA-Seq, cells are polarized for 3 days.

tag: strain/background

value: spleen

tag: time

tag: chip antibody

value: STAT5B (R&D Systems, Sta5B)


title: Th9 72h STAT6

description: ChIP against STAT6.

source_name: Th9 cells, 72h, STAT6 ChIP

tag: tissue

value: STAT6 (Santa Cruz, M-20, sc-981)


title: DNA input

value: Control

tag: strain


title: CT11 DNA

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description: Chromosome territory probe for human chromosome 11

data_processing:
Map to human genome using bwa bwasw
Peak detection using MACS
Genome_build: Grc37
Supplementary_files_format_and_content: CT11 peaks generated with MACS, Repeat content of COT1 generated with custom script

extract_protocol:
Human Cot1 DNA was bought from Invitrogen.  Chromosome 11 painting probe is propietary.
Followed the instruction of Illumina TruSeq ChIP Sample Preparation kit, Set A (IP-202-1012, Illumina). Briefly, Chromosome 11 Painting probes or human cot1 DNA was end repaired and Adenylated 3 ends of DNA fragment.  Indexed adapters are ligated to the DNA fragment. Inserted PCR fragment (250bp-600bp) was purified with agarose gels. Purified product was amplified with Illumina primers for 18 cycles. The amplified fragment was used for cluster generation on the Illumina MiSeq flowcell.  Sequencing was done following the Miseq protocol.

tag: sample type

value: CT11 DNA


title: Th9 72h antiIL2 BCL6

description: ChIP against BCL6.

source_name: Th9 cells, 72h, BCL6 ChIP

tag: cell type

value: BCL6 (Santa Cruz, N-3, sc-858)


title: Th9 72h BCL6

description: ChIP against BCL6.


title: Stra8-KO_rspd

description: The mouse testis is upf2 knockout

value: Upf2 Knockout round sperm cell

tag: age

value: 6 weeks

value: upf2 knockout


title: Th9 0h STAT5B

description: ChIP against STAT5B.

source_name: Th9 cells, 0h, STAT5B ChIP


title: MCF10A-MeRIP rep1 (technical replicate)

city: San Antonio

first: Xiaodong

last: Cui

state: Texas

address: 126 Arrow Oaks

department: Electrical engineering

institute: Univ of Texas SA

data_processing:
library strategy: MeRIP-Seq
llumina Casava1.8 software used for basecalling.
Sequenced reads were first aligned to TopHat.
Peak calling was performed by ExomePeak at FDR < 0.05 with IP/Input Ratio set to 1.
Differential analysis was performd by ExomePeak at FDR < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: bed and xls files

growth_protocol: Human breast cancer cells MDA-MB-468 were grown in (150 mm X 16 cell culture plates) in RPMI medium (Invitrogen) supplemented with 10% fetal bovine serum, anti-anti (Invitrogen). Cells were allowed to grown until reaches 80% confluent were harvested using 0.25% trypsin (Invitrogen).

extract_protocol:
Total RNA was isolated and quantified from the cell culture using QIAZoL(Qiagen Inc.). Next, total RNA was enriched for polyadenylated RNA (polyA mRNA).  Poly A+RNA was chemically fragmented into ~100-nucleotide long fragments. A portion of the fragmented RNA was subjected to RNA-seq that served as input (control). The remaining RNA was subjected to immunoprecipitation (IP) with anti-methyl cytosine antibody.
The isolated, fragmented, and enriched m5C mRNAs were submitted for sequencing library preparation by using standard Illumina TruSeq Sample Preparation Kits, without poly-A purification step
RNA-Seq, 50bp SR by Hiseq 2000

treatment_protocol: No additional treatment was performed to cell cultures

tag: cell line

value: Mammary Epithelial cells

tag: m5c antibody

tag: m5c antibody vendor

value: Zymo Research

tag: m5c antibody cat.#


title: Th9 16h STAT5B

description: ChIP against STAT5B.

source_name: Th9 cells, 16h, STAT5B ChIP


title: MCF10A-MeRIP rep2 (technical replicate)


title: MCF-10A-MeRIP rep2


title: MCF-10A-input rep2


title: Th9 WT RNASeq

description: 2x polarized

data_processing:
For ChIP-Seq and RNA-Seq, basecalls performed using CASAVA 1.8 (HiSeq2000).
Raw reads were aligned to the mm8 (MGSCv36) genome assembly using Bowtie 0.12.4.
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts.
For ChIP-Seq, peaks are called using MACS 1.3.7.1; For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database.
Genome_build: MGSCv36
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.8 and unpublished python scripts, rpkm (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts.

source_name: Th9 cells

growth_protocol: naïve CD4+ T cells from C57/B6 mice were cultured under Th9 condition (10 ug/ml of anti-IFNg, 40 ng/ml of IL-4, 2 ng/ml of TGF-beta, 2 ug/ml of  plate-bound anti-CD3, and 1 ug/ml of anti-CD28)for indicated time.

extract_protocol: For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols. For RNA-Seq, total RNA was extracted from 5x10^6 cells per sample using Rneasy Mini kit (QIAGEN) and the quality and concentration were determined by Nanodrop ND-1000 spectrophotometer. Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor. After repairing ends, adaptor (Illumina) was added using T4 DNA ligase (New England Biolabs), and 220-400 bp fragments were isolated using 2% E-Gel (Invitrogen) and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).

treatment_protocol: For ChIP-Seq,cells treated with Th9 condition for 2 rounds. For RNA-Seq, cells are polarized for 3 days.

tag: genotype/variation

value: wild type


title: Th9 STAT6

description: ChIP against STAT6

source_name: Th9 cells, STAT6 ChIP


title: Th9 IgG

description: ChIP against IgG

value: Rabbit IgG (R&D Systems)


title: Th9 IL2KO RNASeq

description: 2x polarized


title: Th9 STAT5B

description: ChIP against STAT5B

source_name: Th9 cells, STAT5B ChIP

value: STAT5B (R&D Systems)


title: MCF-10A-input rep1


title: MCF-10A-MeRIP rep1


title: COT1 DNA

description: COT1 DNA

value: COT1 DNA


title: Th9 72h STAT5B

description: ChIP against STAT5B.


title: MDA-468-input rep2

value: Human breast cancer cells


title: MDA-468-MeRIP rep2


title: Th9 72h antiIL2 STAT6

description: ChIP against STAT6.


title: b_SF_iPS_1

status: Public on Feb 19 2014

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

data_processing:
Sequencing data was analyzed starting from BCL and CIF intensity files generated by the Illumina Genome Analyzer SCS 2.9/RTA 1.9 software. Ibis 1.1.6 was trained from the φX174 control reads of all lanes aligned to their reference sequence and then used to re-call bases and PHRED-like quality scores from intensity files [PMID: 19682367].
Only reads matching one of the used indexes or one-edit variants [PMID: 20516186] were further processed and subjected to an adapter and chimera filter; removing artifactual sequences and trimming adapter sequence starting at the read end [PMID: 21801405]. From this data, reads with more than 5 bases below a quality score of 15 as well as reads shorter than 60 bases after trimming were discarded.
Human Ensemblv66 gene models for GRCh37 were transferred to the coordinates of the chimpanzee genome (CHIMP2.1.4), the gorilla genome (gorGor3.1) and the rhesus macaque genome (MMUL_1) using Ensembl Compara v66 six primate EPO whole genome alignments. Since this version of Ensembl did not include a chimpanzee mitochondrial genome, the Ensembl Compara mitochondrial alignments were obtained from the v64 release. Further, the CHIMP2.1.4 genome was supplemented by the previously used mitochondrial genome. Exon start and end coordinates where independently transferred using the EPO alignments and only genes were used where (1) all exons and their respective start and end coordinates were assigned to a single chromosome/contig, (2) exons were on the same strand in each single species and (3) adjacent exons were not more than 1 Mb apart in the three species under consideration.
Tophat 1.4.1 [PMID: 19289445] was used to align sequences for each sample first to the inferred transcriptome of each species and the remaining reads to the reference sequence. We also aligned all samples to the mouse annotation (Ensembl v66) and mouse reference genome (musMus37). We removed all reads from the species alignments which aligned with the same or fewer mismatches to the mouse genome.
Gene models were quantified using Cufflinks 1.3.0 [PMID: 21697122] with activated fragment bias correction and correction for reads mapping to multiple genomic locations. For analysis, we only considered genes as detected with an FPKM value greater or equal to the size of the 95% FPKM-confidence interval [PMID: 22068331].
Genome_build: GRCh37, CHIMP2.1.4, gorGor3.1, MMUL_1
Supplementary_files_format_and_content: FPKM values for all ES/iPS samples

molecule: polyA RNA

organism: Pan paniscus

source_name: fibroblast, skin

growth_protocol: All ESC and iPSC lines were cultured and expanded under standard ES-cell culture conditions in ko-DMEM supplemented with 20% knockout serum replacement, 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1% nonessential amino acid stock, and 15 ng/ml (cyiPSCs, goiPSCs, boiPS, MF12, R366.4), 10ng/ml (human iPSCs) and 50 ng/ml (human ESCs) basic fibroblast growth factor (all from Invitrogen, Carlsbad, USA)

extract_protocol:
Cells were grown as described above in 6-well plates, removed from mouse feeder cells as good as possible and cells from one plate suspended in 1ml Trizol (Invitrogen). Total RNA from 500µl Trizol was isolated and further purified using RNAeasy columns (Quiagen).
RNA-Seq libraries were constructed using a custom protocol combining the Illumina TruSeq RNA protocol to generate cDNA and a double-indexing protocol [PMID: 22021376, PMID: 20516186] to generate sequencing libraries from this cDNA (full detailed protocol available upon request). Briefly, 1µg of total RNA was mRNA purified twice (Sera-Mag Magnetic Oligo(dT) beads, Thermo Scientific), cleaned up using RNAClean beads (Beckman Coulter), eluted in 2µl first strand buffer and 0.5µl random primers (Invitrogen) and fragmented for 7 min at 85°C. After first and second strand synthesis, cDNA was end-repaired, custom P5 and P7 adapters were ligated, blunted, quantified and amplified in an indexing PCR essentially as described [PMID: 20516186], except that both ends were indexed [PMID: 22021376]. The quality and concentration of the library were assessed on a BioAnalyzer.

value: iPS


title: b_SF_iPS_2


title: MDA-468-MeRIP rep1


title: m_RESC_ES

organism: Macaca mulatta

source_name: stem cells

value: ES


title: MEFD5_TARRBS_hmC

city: Shanghai

first: Shiqing

last: Mao

address: 320 Yue Yang Road

institute: SIBS

description: MEFs after OKS induction

data_processing:
Illumina Casava1.8 software used for basecalling.
FASTQ reads generated by the Illumina HiSeq2000 platform were subject to Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to trim low quality bases and Illumina adapters.The RRBS option of Trim Galore was activated to remove the disputed 2 bp from the 3’ ends of the reads.
The adapter-free reads were then aligned to the mouse reference genome sequences (mm9) using Bismark program (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) (Krueger and Andrews, 2011).
All cytosine sites were extracted from the mapping results unless it coincided with a record in dbSNP. The 5mC and 5hmC calling were processed as previously described (Yu et al., 2012b).
Analysis of differentially methylated & hydroxymethylated cytosines was accomplished with the R package methylKit (Akalin et al., 2012).
Genome_build: mm9
Supplementary_files_format_and_content: wig files; Scores represent percent of methylation (*mC.wig) or hydroxymethylation (*hmC.wig).

source_name: mouse embryonic fibroblast

extract_protocol:
Genomic DNA was extracted with the DNeasy Blood & Tissue Kit (Qiagen)
The extracted DNA was digested with MspI for 3 hr at 37°C, and purified with QIAquick PCR Purification Kit. Size selection of 75-400 bp DNA fragments was performed by electrophoresis on 3% NuSieve 3:1 agarose gel (Lonza). Gel extracted DNA was mixed with spike-in controls and was split into two aliquots. The portion for TA-RRBS was glucosylated by β-glucosyltransferase, and oxidized with recombinant mouse TET1 protein as previously described (Yu et al., 2012b). The aliquot for RRBS was applied directly to the library generation procedure.DNA samples for RRBS and TA-RRBS were end-repaired, adenylated and ligated to methylated adaptors using Illumina TruSeq Sample Preparation Kits following the manufacturer’s instructions. After bisulfite conversion by the MethylCode Kit (Invitrogen), the ligated fragments were then PCR amplified with PfuTurbo Cx Hotstart DNA polymerase (Agilent). Final libraries were purified with 1× AMPure XP beads and sequenced using Illumina HiSeq 2000.

value: mouse embryonic fibroblast

tag: induction stage

value: Day 5 after OKS induction


title: m_ORMES6_ES


title: MEFD5_RRBS_mC

description: MEFs after OKS induction


title: Pol II_ChIP Seq - WT

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequenced reads were aligned to the yeast sacCer3 genome using bwa with parameter -t 15
Reads were quality trimmed and adapters removed using trimmomatic version 0.22  with parameters ILLUMINACLIP:2:20:10 SLIDINGWINDOW:5:20 HEADCROP:4 MINLEN:20
Reads that align to multiple locations in the genome were removed from downstream analysis
Reads aligning to rDNA regions were removed
Read depths were normalised to reads per million mapped reads to account for varying sequencing depths between samples
Genome_build: sacCer3
Supplementary_files_format_and_content: Bam files were converted to UCSC bigwig format

organism: Saccharomyces cerevisiae

source_name: Yeast WT

growth_protocol: Cells were grown in YPDA medium at 25C and samples were harvested at 25C and after 30 minute shift to 37C.

extract_protocol:
Chromatin extracts were prepared by spheroplasting and passing through ficoll to attain nuclear lysate. This is futher Mnase digested and used to pull down Pol II bound DNA with the antibody.
Library was constructed using standard illumine protocol. Repair ends was performed using (T4 DNA ligase buffer (10x), T4 DNA polymerase (Roche - 12407230), dNTP mix each 10mM, klenow DNA polymerase, T4 PNK (Promega – M410A)  followed by “A” tailing (Klenow buffer, dATP(1mM), klenow (exonuclease 3'-5') enzyme) to prepare the DNA for ligation. Adaptor ligation was performed using (Quick T4 DNA ligase kit). Ligated mixtures were further PCR amplified (18 cycles) and DNA libraries were resolved in the gel. The bands corresponding to the molecular weight between 200 bp-400 bp was gel eluted. Purified libraries were further checked for the presence of the adaptor dimer, average size, quality and quantity using bioanalyser and the qualified ones were subsequently sequenced. Sequencing was performed in the Genepool Seqeuncing facility (University of Edinburgh).

treatment_protocol: Harvested cells were formaldehyde (1%) crosslinked for 10 minutes and quenched with Glycine for 5 minutes

value: Pol II antibody (4F8- HemholtzZentrum münchen )

tag: growth conditions

value: WT strains grown at 25C


title: Pol II_ChIP Seq - prp5-1 (1)

source_name: Yeast MT

tag: antibody

value: MT strains grown at 25C


title: Pol II_ChIP Seq - prp5-1 (2)

value: MT strains grown at 25C and shifted to 37C for 30 min


title: MEF_RRBS_mC

description: MEFs before OKS induction

value: Day 0


title: m_Cyno_iPS_3_rep2

description: replicate

organism: Macaca fascicularis


title: m_MF12_ES


title: m_Cyno_iPS_3_rep1


title: OS-RC-2-RNA-seq

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

data_processing:
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of  RNA sequencing reads were aligned to the reference genome (UCSC hg19) using the SOAP aligner with parameters -m 90 -x 500 -l 15 -s 35 -p 4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
genome build: hg19
processed data files format and content: bed files: contained chromsome,reads strart site,reads end sites;tab-delimited text files include RPKM values for each Sample

growth_protocol: one renal cancer cell line (786-O),another renal cancer cell line OS-RC-2 was from Riken Cell Bank (Tsukuba, Japan). Cells were cultured according to the supplier’s recommendations.

extract_protocol: Total RNA was isolated from 786-O and OS-RC-2 cells using the miRNeasy Kit (Qiagen 74104) according to the manufacturer's protocol. An additional DNaseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. The RNA purity was assessed using the Agilent bioanalyzer. Total RNA was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The cDNA was then used for Illumina sequencing library preparation. DNA fragments were end-repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls, and adapters were ligated for paired-end sequencing on an Illumina HiSeq 2000.

value: renal


title: OS-RC-2-LHC-BS-promoter-seq

description: OS-RC-2-LHC-BS-seq in promoter (Tss up 2200 down 500)

data_processing:
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of LHC-seq reads were mapped to hg19 BSMAP using default parameters.
Using unique mapped reads, and after duplication reads (the pair end mapped reads share same postion only use the best mapped pair reads to eliminate the affect of PCR). then extract the methylation of CpG and the read densi  ty of each sample. we further analysis the enrichment of each sample using RSEG software(0.4.4) the parameter using default with bin size 500bp and posterior cutoff 0.95.
genome build: hg19
processed data files format and content: bed files:it contained chromsome,reads strart site,reads end sites,methyl information of each CpG

growth_protocol: Cells were cultured according to the supplier’s recommendations.

extract_protocol:
The liquid hybridization capture procedure was performed as follows. Briefly, 200 ng DNA from each of five adapter-ligated libraries were pooled together. 10 µg human Cot-1 DNA and 1nmol of adapter complementary DNA oligos were added and subsequently were dried using a SpeedVac (eppendorf) at 60°C. After that, the mixture was denatured at 95°C for 10min in a final reaction volume of 10.5µl consisting of 7.5µl 2X SC Hybridization Buffer and 3µl SC Hybridization Component A. After centrifugation, 4.5µl of designed probes were added and the mixture was hybridized in a thermal cycler at 47°C for 72 hours with the lid heated at 57°C. After hybridization, the biotinylated probes which had bind the target DNA were captured using 100µl of Dynabeads® M-280 Streptavidin (Invitrogen), which had been pre-washed two times with a total of 400µl Streptavidin Dynabead Binging and Washing Buffer. The capture program was 47°C for 45min in a thermal cycler with the lid heated at 57°C and vortexing for 3 seconds at 15min intervals. Discarded the unbounded fractions and washed the collected DNA-probe-beads complex with 100µl of 47°C pre-warmed 1X Wash Buffer I for one time and with a total of 400µl of 47°C pre-warmed 1X Stringent Wash Buffer I for two times with the incubations of 47°C for 5min. After discarded the supernatant, the collected beads complex was again washed with 200µl of 1X Wash Buffer I, 1X Wash Buffer Ⅱ and 1X Wash Buffer Ⅲ respectively. Finally, the captured DNA was eluted in 50µl of 10M NaOH with incubation at room temperature for 10min. The supernatant was transferred into a new tube and neutralized with 50µl of 10M HAc and then purified using MiniElute PCR purification Kit (Qiagen).For bisulfite conversion, 200ng unmethylated lambda DNA was added into each captured product as carriers and ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO) was employed to convert unmethylated cytosine into uracil according to the instructions. After purification, PCR was carried out in a final reaction volume of 50µl consisting of 20µl converted products, 4µl 2.5mM dNTP, 5µl 10×buffer, 0.5µl JumpStart™ Taq DNA Polymerase (SIGMA), 1µl PCR primers1.0, 1µl PCR index primers (which were used to identify different captures) and 18.5µl water. The following thermal cycling program was 94°C 1 min, 15 cycles of 94 °C 10s, 58°C 30s, 72°C 30s then prolong at 72°C for 5min and hold at 12°C. The PCR products were purified using AMPure beads (Agencourt), quantified by the Bioanalyzer analysis system (Agilent) and real time PCR assay and then analyzed using Illumina Hiseq2000.
Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen). 1µg of genomic DNA was fragmented into approximately 200-300bp using a Covarias sonication system (Covarias). After purification, the fragmented fractions were treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair blunt and phosphorylate ends. The blunt DNA fragments were subsequently 3’ adenylated using Klenow Fragment (3’-5’ exo-) and then ligated by T4 DNA Ligase to adapters that were synthesized with 5’-methylcytosine instead of 5’-cytosine and contain index sequences inside. After each step, the reaction products were purified using QIAquick PCR purification kit (Qiagen). The constructed libraries were quantified using a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen).

value: renal cancer cell line


title: 786-O-RNA-seq


title: h_I4_ES


title: h_LF_iPS_rep1

source_name: fibroblast, lung


title: m_Cyno_iPS_1


title: h_LF_iPS_rep2

description: replicate


title: h_h_3_ES


title: MDA-468-input rep1


title: h_h_I3_ES


title: T24-LHC-BS-promoter-seq

description: T24-LHC-BS-seq in promoter (Tss up 2200 down 500)

value: bladder cancer cell lines


title: g_SF_iPS_6

organism: Gorilla gorilla

source_name: endothelial cells, vein


title: h_CBEC_iPS_2

source_name: endothelial cells, cord blood


title: NCl-H1395-LHC-BS-promoter-seq

description: NCI-H1395-LHC-BS-seq in promoter (Tss up 2200 down 500)

value: lung cancer cell lines


title: HCC827-LHC-BS-promoter-seq

description: HCC827-LHC-BS-seq in promoter (Tss up 2200 down 500)


title: AGS-LHC-BS-promoter-seq

description: AGS-LHC-BS-seq in promoter (Tss up 2200 down 500)

source_name: AGS-LHC-BS-promoter-seq

value: stomach  epithelial cells


title: 786-O-LHC-BS-promoter-seq

description: 786-O-LHC-BS-seq in promoter (Tss up 2200 down 500)


title: MEF_TARRBS_hmC

description: MEFs before OKS induction

source_name: MEF_Tet-Assited RRBS


title: g_SF_iPS_4


title: h_CBEC_iPS_1


title: 5637-LHC-BS-promoter-seq

description: 5637-LHC-BS-seq in promoter (Tss up 2200 down 500)

value: bladder cells


title: g_SF_iPS_2_rep1


title: m_Cyno_iPS_2


title: g_SF_iPS_3_rep2

description: replicate


title: BGC-823-LHC-BS-promoter-seq

description: BGC-823-LHC-BS-seq in promoter (Tss up 2200 down 500)


title: YH-LHC-BS-promoter-seq

description: YH-LHC-BS-seq in promoter(Tss up 2200 down 500)

source_name: YH-LHC-BS-promoter-seq

value: lymphoblastoid cells


title: YH-rep-LHC-BS-promoter-seq

description: repeat YH-LHC-BS-seq in promoter(Tss up 2200 down 500)

source_name: YH-rep-LHC-BS-promoter-seq


title: g_SF_iPS_2_rep2

description: replicate


title: g_SF_iPS_1


title: 97H mRNA

status: Public on Feb 18 2014

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

description: total polyA+ mRNA

data_processing:
The sequencing reads were mapped to the Ensembl-v72 RNA reference sequences using FANSe2 algorithm (http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters of –L55 –E3 –S14. Alternative splice variants were merged.
The genes with at least 10 mapped reads were deemed confident gene identification and quantification
Gene expression levels within a single cell line were calculated using the rpkM method
The differential expression level across cell lines were performed using edgeR software package
Genome_build: hg19 (Ensembl-v72 RNA reference sequence)

growth_protocol: Human liver carcinoma cell lines, including Hep3B, HCC-LM3 (LM3) and MHCC-97H (97H) cells, cells were obtained from American Type Culture Collections (ATCC, Rockville, MD, USA).  LM3 and 97H cells were maintained in complete DMEM media (Invitrogen, Carlsbad, CA, USA), supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen) and 10 μg/mL ciprofloxacin. Hep3B cells were cultured in complete MEM media (Invitrogen), supplemented with 15% FBS, 1 mM sodium pyruvate, 1% penicillin/streptomycin (Invitrogen) and 10 μg/mL ciprofloxacin

extract_protocol:
mRNA and RNC-mRNA was extracted according to the literature "Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific" Nucleic Acids Res. 2013
The library was constructed by using NEBNext mRNA Sample Prep Master Mix Set for Illumina

value: hepatocellular carcinoma cell line

tag: strategy

value: mRNA


title: 97H RNC-mRNA

description: polyA+ mRNA bound to ribosome

value: RNC-mRNA


title: Hep3B mRNA

description: total polyA+ mRNA


title: LCL_TRF2_S6

city: Philadelphia

first: Nicholas

last: Stong

state: Pennsylvania

address: 3600 Spruce St

institute: Wistar Institute/UPenn

data_processing:
Basecalls performed Illumina CASAVA version 8
ChIP-Seq reads were trimed to first high quality base and mapped to a custom reference genome humanhg19Hybrid using BWA 0.6.2 -n 101
Fragment size was estimated using cross strand correlation and fragment densities built across the genome using a moving average.  Signal track was generated as fold enrichment over IGG
Peak calls were made using MACS 2.0.10,  bdgcmp –m ppois and bdgpeakcall –l 50 –c 4
Reads were analysed using RepeatMasker and those containing (CCCTAA)n were removed and analysis was performed again, lower cutoff used to select peaks
Genome_build: humanhg19Hyrbid
Supplementary_files_format_and_content: bedGraph fragment fold enrichment and encodePeak peak calls, for both all reads, and (CCCTAA)n removed

source_name: LCL

growth_protocol: LCL cells were grown to 1x10^6 cells/ml in RPMI with 15% FBS supplemented with Glutamax and Penn/Strep.

extract_protocol:
Lysates were clarified from sonicated nuclei, and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions.
Libraries were prepared according to Illumina's ChIPSeq Sample Prep. protocol (IP-102-1001).  Briefly, DNA was end-repaired to produce blunt ends,  adenylated for 'A' base addition to the 3' end and then adapter ligated. The adapter ligated DNA was size-selected on an Agarose gel and purified. The purified DNA was enriched by 18 cycles of PCR yielding library fragments of ~290  (insert plus adaptor sequence).  The libraries were subjected to hybridisation onto the flowcell for cluster generation and finally sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

value: LCL


title: LM3 RNC-mRNA

description: polyA+ mRNA bound to ribosome


title: LCL_IGG_S8

value: IgG


title: LCL_TRF1_S5


title: Caco-2 RNC-mRNA

description: polyA+ mRNA from RNC-RNA

data_processing:
High quality reads which passed the Illumina filter were mapped with FANSe2 algorithm (http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters –L55 –E5 –U0 –S10
Reference sequence: NCBI RefSeq-RNA reference sequence (downloaded from from http://hgdownload.cse.ucsc.edu/downloads, accessed on Jan. 21st, 2013)
Genome_build: hg19
Supplementary_files_format_and_content: Caco-2 rpkM: rpkM of mRNA and RNC-mRNA

source_name: Caco-2 cell line

growth_protocol: Human Caco-2 cells were obtained from American Type Culture Collections (ATCC, Rockville, MD). Cells were cultured in complete DMEM media  (Invitrogen, Carlsbad, CA), supplemented with 10% fetal bovine serum (FBS) (PAA Australia, Weike Biochemical Reagent, Shanghai, China), 1% penicillin/streptomycin and 10 μg/mL ciprofloxacin.

extract_protocol:
See the paper " Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific" Wang et. Al. NAR 2013. Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina). The mRNA was fragmented by incubation in Elute-Prime-Fragment Mix at 94°C for 8 min to obtain 120–200 bp inserts
See the paper " Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific" Wang et. Al. NAR 2013. Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina). The mRNA was fragmented by incubation in Elute-Prime-Fragment Mix at 94°C for 8 min to obtain 120–200 bp inserts. First-strand cDNA was synthesized with SuperScript II Reverse Transcriptase (Invitrogen) using random primer, and Ampure XP beads (Beckman Coulter, Beijing, China) were used to isolate double-stranded cDNA synthesized by Second Strand Master Mix. The adapters were ligated to the A-Tailing fragment, and 12 cycles of PCR were performed to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Invitrogen) and validated by Agilent 2100 bioanalyzer (Agilent, Beijing, China). Clusters were generated by cBot with the library diluted to 10 pM


title: Hep3B RNC-mRNA

description: polyA+ mRNA bound to ribosome


title: LM3 mRNA

description: total polyA+ mRNA


title: Caco-2 mRNA

description: polyA+ mRNA from total RNA


title: Stage 5 validation

city: Los Angeles

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

data_processing:
reseq_stage5_CT_a.pileup; genome build: UCSC dm3
reseq_stage5_CT_b.pileup; genome build: UCSC dm3
reseq_stage5_GA_a.pileup; genome build: UCSC dm3
Read calling and alignment. Illumina raw data were  processed with Illumina's Pipeline 1.3.2, skipping the first two cycles (corresponding to the portion of the HpyCH4III recognition site that was left after restriction digestion) to facilitate cluster identification. The first 9 nucleotides of each read, corresponding to the C in the adapter following the HpyCH4III site and the first 8 bases of the random primer, showed higher error rates than the remaining 25 nucleotides and were trimmed prior to sequence alignment. Paired reads were aligned to the  drosophila reference genome assembly (version dm3 from the UCSC Genome Bioinformatics site, using all the chromosomes except Uextra) using Novoalign v2.07.06 run in bisulfite mode. Novoalign was run with the following options: -t 90 -h 120 -r A 3 -k; these options allow a set of paired reads to align with up to (approximately) 3 mismatches over the combined length of the two reads, and report up to 3 alignments for reads generating more than one optimal alignment. The forward (CT) and reverse (GA) stands of DNA become non-complementary following bisulfite conversion. Novoalign in bisulfite mode  can align bisulfite treated sequences against a reference genome in a single pass that aligns against both CT and GA in-silico indexed reference sequences.    Identification of methylated cytosines. Unconverted (methylated) cytosines will be read as 'C' if the sequence is derived from the CT strand, and as 'G' if the sequence is derived from the GA strand. Conversely, a 'C' from the GA strand and a 'G' from the CT strand correspond to a guanine in the reference sequence and must be ignored in the analysis. The loss of complementarity following bisulfite conversion makes it possible to determine if a methylated cytosine is on the CT or the GA strand. This is important if methylated sequences are asymmetric (i.e. non-CG methylation). To determine if a sequence alignment is derived from the CT or GA strand, we implemented the following decision tree: 1- if an alignment  has only CT or GA mismatches, it is assigned to the respective strand if the corresponding number of CT or GA mismatches is at least 2; otherwise, the read is considered ambiguous and further processed in step 3; 2- if an alignment has both CT and GA mismatches, it is assigned to the strand that has at least a 2-fold excess of one type of mismatch; otherwise, the read is considered ambiguous and further processed in step 3; 3- if an ambiguous alignment is primary and in a proper pair, the strand assignment of the mate pair is transferred to the ambiguous read; otherwise the ambiguous alignment is discarded; 4- alignments that are primary, in a proper pair, and not containing an ambiguous strand assignment, are checked for consistent strand assignment (i.e.: both mate pairs are assigned to the same strand). If the assignment is inconsistent, the pair is discarded.    Generation of "medip-bis_PE-tr9_d2_CT-PE.pileup" and "medip-bis_PE-tr9_d2_GA-PE.pileup" files: following strand assignment of all alignments, we calculated pileup files for the CT and GA strands from their respective alignments files. We used a modified pileup program that does not ignore  any reads in the alignment: reads with multiple alignments and reads not mapped in proper pair are included in the output. We identified methylated cytosines on the CT and GA strands separately, by counting (from the pileup files)  how many alignments contained either a 'C' or a 'T' at C positions on the CT strand, and  how many alignments contained either a 'G' or an 'A' at G positions on the GA strand. From here onwards we refer to C positions on the CT strand and G positions on the GA strand as “methylated cytosines”.  Identification of methylated regions.  We first selected cytosines with strong evidence of methylation by retaining only those methylated cytosines at which at least three alignments had an unconverted C and the ratio of C-containing alignments over the sum of C- and T-containing alignments was greater than 0.1. These criteria remove cytosines with methylation supported by only one or two reads or where the vast majority of the reads do  not support the presence of methylation. It is likely that these filtering steps remove cytosines with low levels of methylation.Generation of "box25_d2_AG_count_3_ratio_0.1.bed"  and "box25_d2_TC_count_3_ratio_0.1.bed" files: we used all methylated cytosines passing the filter above to identify regions of high methylation. We divided the genome into segments of 25 nucleotides and counted how many methylated cytosines were within each segment. Segments without any methylated cytosine were discarded, and contiguous segments with at least one methylated cytosine were merged. Finally, we retained for analysis only segments in which the underlying alignments contained at least 25 methylated cytosines.
Read calling and alignment of bisulfite PCR sample.  Sequence reads were aligned to a reference sequence consisting of the regions that were targeted for amplification using Novoalign v2.07.11 run in bisulfite mode with the -g200 option.  After bisulfite conversion, PCR amplifies one of the two DNA strands (labeled 'CT' and 'GA'), the one against which the PCR primers are designed. Only reads aligning against the correct DNA strand were further processed. We used a modified pileup program (that retains reads with multiple alignments) to determine the degree of methylation at all cytosines. Cytosine positions at which the total count of converted and unconverted cytosines was less than 90% where discarded as potentially polymorphic.
We used the sequences from the lambda phage to asses the efficiency of bisulfite conversion.

organism: Drosophila melanogaster

source_name: whole embryo

extract_protocol:
Immunoprecipitation and bisulfite conversion of methylated DNA. Genomic DNA was isolated from syncronized Stage 5 (2-3 hours) embryos of Canton-S Drosophila melanogaster. Methylated DNA fragments, obtained by sonication of 2 μg of Stage 5 DNA (fragment size range: 100–700 bp), were immunoprecipitated by overnight incubation at 4°C with 5 μg of monoclonal antibody against 5-methylcytidine (Eurogentec, Cat #: BI_MECY_0100, Lot #: 070927) following the manufacturer's instructions. Antibody-DNA complexes were recovered with Dynabeads M-280 Sheep anti-Mouse IgG (Dynal Biotech), washed twice in IP buffer, once in high salt buffer, and twice in TE buffer. Washed complexes were incubated overnight with Proteinase K. Immunoprecipitated DNA was collected from the supernatant with the Qiaquick PCR purification kit (QIAGEN) and converted with sodium bisulfite using the EpiTect Bisulfite Kit (QIAGEN) following the manufacturer’s instruction. PCR amplification and sequencing library construction. DNA is single stranded following bisulfite conversion. To make DNA double-stranded and generate enough material for constructing a sequencing library, we performed a random-primed PCR amplification. Bisulfite converted DNA was subjected to a round of linear amplification using an adapter combined with a random 9-nucleotide primer (GTT TCC CAG TCA CGG TC(N)9), purified, and PCR-amplified using primers against the adapter sequences. The PCR reaction was purified with MinElute PCR Purification Kit (QIAGEN) and digested with HpyCH4III (NEB) to remove the adapter sequences. The digest was resolved on a 2% agarose gel; the smear in the range of 100 to 500 bp was excised, purified with Gel Extraction Kit (QIAGEN), and used for library construction with the ChIP-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions. The library was sequenced on an Illumina GAII to collect paired-end reads of 36 nucleotides each.
Preparation of libraries for bisulfite PCR sequencing. Genomic DNA from synchronized stage 5 (2-3 hours) embryos of Oregon R D. melanogaster and equimolar of unmethylated lambda DNA (Promega) were bisulfite treated with Methyleasy Xceed kit (Human Genetic Signature), and 5 to 20 ng of treated DNA were used to amplify specific target regions in the Drosophila and lambda genomes with PCR primers designed to prime completely converted (i.e. unmethylated) DNA; this primer design is biased against methylation in the primer binding sites. The amplified products were gel purified and fragmented with Fragmentase (NEB). An Illumina sequencing library was constructed with paired-end adapters following the paired-end protocol, and single read sequencing was carried out with an Illumina GAIIx.
Libraries were constructed with paired-end adapters following Illumina's paired-end protocol

treatment_protocol: All libraries were bisulfite converted with the MethylEasy Exceed kit from Human Genetic Signatures

value: R

tag: developmental stage

value: 2-3h embryo (Stage 5)

value: whole embryo


title: g_SF_iPS_3_rep1

value: iPS


title: XPD_ChIP_Seq

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

description: Sample 2

data_processing:
Base calls were made using Illumina RTA 1.5
Raw reads were trimmed to 60 bp and filtered to remove pairs of reads in which either mate contained 3 or more base calls with a PHRED score below 20. Trimmed, filtered reads were aligned to the hg19 human genome using Bowtie v0.12.7 with settings -n 0 -m 1 --chumkmbs=256 -S to SAM format
A fragment map in bedGraph format was generated using a Perl script that treated paired end reads as the boundaries of IPed fragments. For Input controls, an equal number of fragments from the Input pool were randomly selected to match the number of enriched fragments for XPB or XPD. This fragment map was converted to binary bigWig format using the UCSC bedGraphtobigWig tool.
Peaks were called using MACS v1.4 with a p-value < 1e-15
Summits were located in peaks using a Perl script that searched for the highest point of fragment overlap in each peak.
Genome_build: hg19
Supplementary_files_format_and_content: A fragment map in bedGraph format was generated using a Perl script that treated paired end reads as the boundaries of IPed fragments. This fragment map was converted to binary bigWig format using the UCSC bedGraphtobigWig tool. Scores represent the number of fragments overlapping each genomic position.

growth_protocol: HT1080 cells were cultured in Minimum Essential Medium Eagle, Alpha Modification (MEM-alpha) supplemented with 5% FBS, penicillin, and streptomycin.

extract_protocol: Nuclei crosslinked with 5% formaldehyde were sonicated and precleared with crosslinked Staph A cells. ChIPs were performed with a 1:200 dilution of mouse monoclonal 1B1 directed against the N-terminus of CSB (Hua-Ying Fan, University of Pennsylvania) precipitated using Protein G Dynabeads (Invitrogen). The input sample was digested with RNase, protease, and decrosslinked without enrichment by ChIP. The input sample was digested with RNase, protease, and decrosslinked without enrichment by ChIP. The ends of the ChIP and input samples were repaired using End-It (Epicentre), A-tailed using Taq polymerase (Invitrogen), and Illumina paired-end sequencing adapters were ligated using Quick T4 DNA Ligase (NEB). DNA fragments ranging from 400 to 700 bp were selected and purified by PAGE, then preamplified for 9 (input) or 12 cycles (ChIP) using Illumina paired-end preamplification primers and BioRad iTaq supermix. The preamplified samples were purified using a Qiagen PCR Cleanup kit and sequenced on the Genome Analyzer.

value: Fibrosarcoma cells

value: Rabbit Polyclonal anti-XPD

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: Input_DNA

description: Sample 3

tag: chip antibody


title: TL_rep3

status: Public on Feb 17 2014

city: Coventry

first: Andrew

last: Blanks

address: Clifford Bridge Road

department: Warwick Medical School

institute: University of Warwick

data_processing:
We used Tophat to map paired-end reads for each sample against hg19 using UCSC hg19 genes.gtf reference transcriptome from the 2013 archive. The expected (mean) inner distance between mate pairs (-r) was set at 120.
We used HTSeq to generate count data for transcript_ids using the intersection-nonempty mode. We converted these to a normalised relative abundance (transcripts per million, tpms) for use in further analyses.
We used cufflinks (cuffdiff) to find putative novel transcript variants.
Genome_build: hg19
Supplementary_files_format_and_content: In Human_myometrium_gene_transcript_abundances.xlsx q1 and q2 in the cuffdiff_mergedref and cuffdiff_UCSCref worksheets are as follows:
q1 refers to the TNL samples (term not in labour)
q2 refers to the TL samples (term in labour)

source_name: uterus

extract_protocol:
Human uterine biopsies were harvested, flash frozen in liquid nitrogen and stored. RNA was extracted using RNA-Stat60 and purified. RNA quality was assessed for a RIN score greater than or equal to 6.
Illumina TruSeq RNA Sample Prep Kit was used with 4 ug of total RNA to construct libraries for sequencing.

tag: tissue

value: myometrium

tag: pregnancy state

value: term in labour


title: WI-38 cells with pBABE /Zeo vector #2

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description:
miRNA-seq
CWC

data_processing:
The Firecrest, Bustard and Gerald analysis module (Illumina) were used for image analysis, base calling and filtering the raw data (36 bp reads) from each run to generate the sequence reads.
These sequences were further filtered to contain the pattern N{18,30})CTGTAG where CTGTAG is the 3' adapter.
Sequences passed filters were clustered and technical replicates were combined.
Clustered Sequences were mapped to known human microRNAs from  from miRbase 2008 using BLAST.
Genome_build: Known human miRNAs from miRbase version 11.0
Supplementary_files_format_and_content: Known_miRNA_Count_CWB_CWC_Q_all.txt is a tab delimited text file with counts information for each mapped miRNA. Column CWB/CWC/Q means the number of miRNAs mapped to treatment CWB/CWC/Q, and totalReadsCWB/totalReadsCWC/totalReadsQ means total number of reads passed filter 18-30bp followed by 6bp 3' linker for treatment CWB/CWC/Q i.e., sequence depth for each treatment.
CWB: WI-38 cells infected with BRAFV600E
CWC: WI-38 cells infected with Empty retroviral vectors
Q: WI-38 cells, quiescent

source_name: WI-38 cells with pBABE /Zeo vector

growth_protocol: WI-38 cells were grown in DMEM with 10% FBS and Pen-Step at 37 C under 5% CO2 condition

extract_protocol: Illumina small RNA library protocol

treatment_protocol: WI-38 cells were either infected with BRAFV600E or Empty retroviral vectors and small RNA were prepared from these cells. As an additional control, WI-38 cells were serum starved and used to generate quiscent cells, which were also used to prepase small RNA.

tag: cell type

value: Primary human fibroblast

value: control [empty retroviral vector]


title: WI-38 cells serum starved for 48 hrs

description:
miRNA-seq
Q

source_name: WI-38 cells serum starved fro 48 hrs

value: control [serum starved]


title: XPB_ChIP_Seq

description: Sample 1

value: Rabbit Polyclonal anti-XPB

value: Novus Biologicals


title: WI-38 cells with pBABE /BRAV600E#1

description:
miRNA-seq
CWB

source_name: WI-38 cells with pBABE /BRAV600E

value: infected with BRAFV600E


title: TL_rep4


title: WI-38 cells with pBABE /Zeo vector #1

description:
miRNA-seq
CWC


title: TL_rep5


title: WI-38 cells with pBABE /BRAV600E#2

description:
miRNA-seq
CWB

source_name: WI-38 cells with pBABE /BRAFV600E


title: TL_rep1


title: TNL_rep5

value: term not in labour


title: Stage 5 whole genome

data_processing:
medip-bis_PE-tr9_d2_CT-PE.pileup; genome build: UCSC dm3
medip-bis_PE-tr9_d2_GA-PE.pileup; genome build: UCSC dm3
box25_d2_AG_count_3_ratio_0.1.bed; genome build: UCSC dm3
box25_d2_TC_count_3_ratio_0.1.bed; genome build: UCSC dm3
Read calling and alignment. Illumina raw data were  processed with Illumina's Pipeline 1.3.2, skipping the first two cycles (corresponding to the portion of the HpyCH4III recognition site that was left after restriction digestion) to facilitate cluster identification. The first 9 nucleotides of each read, corresponding to the C in the adapter following the HpyCH4III site and the first 8 bases of the random primer, showed higher error rates than the remaining 25 nucleotides and were trimmed prior to sequence alignment. Paired reads were aligned to the  drosophila reference genome assembly (version dm3 from the UCSC Genome Bioinformatics site, using all the chromosomes except Uextra) using Novoalign v2.07.06 run in bisulfite mode. Novoalign was run with the following options: -t 90 -h 120 -r A 3 -k; these options allow a set of paired reads to align with up to (approximately) 3 mismatches over the combined length of the two reads, and report up to 3 alignments for reads generating more than one optimal alignment. The forward (CT) and reverse (GA) stands of DNA become non-complementary following bisulfite conversion. Novoalign in bisulfite mode  can align bisulfite treated sequences against a reference genome in a single pass that aligns against both CT and GA in-silico indexed reference sequences.    Identification of methylated cytosines. Unconverted (methylated) cytosines will be read as 'C' if the sequence is derived from the CT strand, and as 'G' if the sequence is derived from the GA strand. Conversely, a 'C' from the GA strand and a 'G' from the CT strand correspond to a guanine in the reference sequence and must be ignored in the analysis. The loss of complementarity following bisulfite conversion makes it possible to determine if a methylated cytosine is on the CT or the GA strand. This is important if methylated sequences are asymmetric (i.e. non-CG methylation). To determine if a sequence alignment is derived from the CT or GA strand, we implemented the following decision tree: 1- if an alignment  has only CT or GA mismatches, it is assigned to the respective strand if the corresponding number of CT or GA mismatches is at least 2; otherwise, the read is considered ambiguous and further processed in step 3; 2- if an alignment has both CT and GA mismatches, it is assigned to the strand that has at least a 2-fold excess of one type of mismatch; otherwise, the read is considered ambiguous and further processed in step 3; 3- if an ambiguous alignment is primary and in a proper pair, the strand assignment of the mate pair is transferred to the ambiguous read; otherwise the ambiguous alignment is discarded; 4- alignments that are primary, in a proper pair, and not containing an ambiguous strand assignment, are checked for consistent strand assignment (i.e.: both mate pairs are assigned to the same strand). If the assignment is inconsistent, the pair is discarded.    Generation of "medip-bis_PE-tr9_d2_CT-PE.pileup" and "medip-bis_PE-tr9_d2_GA-PE.pileup" files: following strand assignment of all alignments, we calculated pileup files for the CT and GA strands from their respective alignments files. We used a modified pileup program that does not ignore  any reads in the alignment: reads with multiple alignments and reads not mapped in proper pair are included in the output. We identified methylated cytosines on the CT and GA strands separately, by counting (from the pileup files)  how many alignments contained either a 'C' or a 'T' at C positions on the CT strand, and  how many alignments contained either a 'G' or an 'A' at G positions on the GA strand. From here onwards we refer to C positions on the CT strand and G positions on the GA strand as “methylated cytosines”.  Identification of methylated regions.  We first selected cytosines with strong evidence of methylation by retaining only those methylated cytosines at which at least three alignments had an unconverted C and the ratio of C-containing alignments over the sum of C- and T-containing alignments was greater than 0.1. These criteria remove cytosines with methylation supported by only one or two reads or where the vast majority of the reads do  not support the presence of methylation. It is likely that these filtering steps remove cytosines with low levels of methylation.Generation of "box25_d2_AG_count_3_ratio_0.1.bed"  and "box25_d2_TC_count_3_ratio_0.1.bed" files: we used all methylated cytosines passing the filter above to identify regions of high methylation. We divided the genome into segments of 25 nucleotides and counted how many methylated cytosines were within each segment. Segments without any methylated cytosine were discarded, and contiguous segments with at least one methylated cytosine were merged. Finally, we retained for analysis only segments in which the underlying alignments contained at least 25 methylated cytosines.
Read calling and alignment of bisulfite PCR sample.  Sequence reads were aligned to a reference sequence consisting of the regions that were targeted for amplification using Novoalign v2.07.11 run in bisulfite mode with the -g200 option.  After bisulfite conversion, PCR amplifies one of the two DNA strands (labeled 'CT' and 'GA'), the one against which the PCR primers are designed. Only reads aligning against the correct DNA strand were further processed. We used a modified pileup program (that retains reads with multiple alignments) to determine the degree of methylation at all cytosines. Cytosine positions at which the total count of converted and unconverted cytosines was less than 90% where discarded as potentially polymorphic.
We used the sequences from the lambda phage to asses the efficiency of bisulfite conversion.

tag: strain

value: Canton-S


title: TNL_rep4


title: HB27Δago-2

city: Wageningen

first: daan

middle: christianus

last: swarts

address: Dreijenplein 10

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

description:
Linker has barcode ATCACG
RNA-seq, BaseClear B.V., The Netherlands

data_processing:
Linkers removed by BaseClear B.V., The Netherlands
Reads mapped on Thermus thermophilus HB27 chromosome AND Thermus thermophilus HB27 pTT27 megaplasmid using Rockhopper
Relative expression of genes calculated by comparing averages of total counts for each gene
Genome_build: AE017221 and AE017222
Supplementary_files_format_and_content: Text file with counts per annotated gene. Relative expression of genes in each strain calculated using averages of counts.

organism: Thermus thermophilus HB27

source_name: Cells

growth_protocol: OD600=0.5 --> RNA isolation

extract_protocol:
miRVana isolation kit (Ambion)
Libraries were prepared using standard illumina protocols

treatment_protocol: Cells harvested by centrifugation

tag: genotype

value: ago ko

tag: temperature


title: TNL_rep3


title: TNL_rep2


title: TNL_rep1


title: Input DNA

city: Charlottesville

first: R. Ariel

last: Gomez

state: VA

institute: University of Virginia

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied.
Sequences (50 nt reads, single end) were aligned to the mouse genome (mm9) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3'-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic "signal maps") were stored in BAR files.
Peak locations were determined using the SICER algorithm (v1.1) with a cutoff of FDR = 1E-10 and a Gap size of 3x fragment size (200 bp) for H3K27me3 and 1x fragment size for H3K4me3.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BAR = Signal map of fragment densities in binary format (Affymetrix BAR format).
Supplementary_files_format_and_content: BEDGRAPH = Standard bedGraph file containing SICER islands (peak regions).

source_name: spleen, WT, input

extract_protocol:
Spleens were removed from the mice, snap frozen in liquid N2 and stored at -80°C until shipment on dry ice to ActiveMotif. For fixation, spleens were cut into small pieces in PBS + 1% formaldehyde and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycin (final) and tissue pieces were treated with a TissueTearer. Chromatin was isolated by disrupting the cells with a Dounce homogenizer. Lysates were sonicated using a Misonix Sonicator 3000 equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and stored at -80 C. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNaseA, proteinase K and heat for de-crosslinking, followed by phenol/chloroform extraction and ethanol precipitation. Purified DNA was quantified on a NanoDrop spectrophotometer. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using precleared chromatin and antibodies and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. Immune complexes were eluted from the beads with SDS buffer, and subjected to RNase treatment and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3'-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (250-350 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

tag: strain/background

value: RBP-J +/+;Ren1dcre/+

tag: age

value: 261 days

tag: tumors

value: no

value: spleen


title: MU_H3K4me3_ChIPSeq

source_name: spleen, RBP-J mutant, H3K4me3 ChIP

value: RBP-J flox/flox;Ren1dcre/+

value: 253 days

value: yes

value: H3K4me3 (Active Motif Cat.#39159 Lot.4)


title: HB27-2

description:
Linker has barcode ATGTCA
RNA-seq, BaseClear B.V., The Netherlands

value: wt


title: WT_H3K27me3_ChIPSeq

source_name: spleen, WT, H3K27me3 ChIP

value: H3K27me3 (Millipore Cat.#07-449 Lot. JBC1854858)


title: WT_H3K4me3_ChIPSeq

source_name: spleen, WT, H3K4me3 ChIP


title: TL_rep2

value: myometrium

value: term in labour


title: MU_H3K27me3_ChIPSeq

source_name: spleen, RBP-J mutant, H3K27me3 ChIP