title: HudsonAlpha_ChipSeq_SK-N-SH_ELF1_(SC-631)_v042211.1

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin. Antibody Target:ELF1

value: This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq)

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin. Antibody Target: ELF1


title: HudsonAlpha_ChipSeq_HepG2_NRSF_v041610.1

status: Public on Sep 28 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Mouse monoclonal. Antibody Target:NRSF

tag: antibody targetdescription

value: Neuron-restrictive silencer transcription factor

tag: antibody vendorname

value: Dr. David Anderson at Caltech

tag: antibody vendorid

value: (Made by Protein Expression Center:pec@caltech.edu)

tag: controlid

tag: labexpid

tag: softwareversion

value: MACS

tag: cell sex

value: M

tag: antibody

value: NRSF

value: David Anderson, Caltech

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: protocol

tag: protocol description

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)

tag: replicate


title: HudsonAlpha_ChipSeq_A549_NRSF_EtOH_0.02pct_v042211.1

value: 1 h with 0.02% Ethanol (Myers)

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)


title: HudsonAlpha_ChipSeq_ECC-1_ERalpha_a_BPA_100nM_v041610.2

value: Rabbit affinity purified polyclonal antibody. Epitope is the C-terminus of human estrogen receptor alpha (ESR1). Recommended for detection of estrogen receptor of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:ESR1

value: This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq)

value: Santa Cruz Biotechnology

value: 1 h with 100 nM Bisphenol A (Myers)

value: 1 h with 100 nM Bisphenol A  (Myers)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_A549_TCF12_EtOH_0.02pct_v042211.1

value: ChipSeq

value: Chromatin IP Sequencing

value: HEB (A-20) Rabbit polyclonal IgG, 200 ?g/ml. Epitope mapping within the C-terminus of HEB of human origin. Antibody Target:TCF12

value: The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.


title: HudsonAlpha_ChipSeq_PANC-1_NRSF_v041610.1

value: Mouse monoclonal. Antibody Target:NRSF

value: Neuron-restrictive silencer transcription factor

value: Dr. David Anderson at Caltech

value: (Made by Protein Expression Center:pec@caltech.edu)

value: MACS

value: M


title: HudsonAlpha_ChipSeq_HepG2_NFIC_(SC-81335)_v042211.1

value: Mouse monoclonal IgG, raised against a recombinant protein corresponding to an internal region of NF-1 of human origin. Antibody Target:NFIC

value: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.

value: No special treatment or protocol applies

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)


title: HudsonAlpha_ChipSeq_GM12878_NRSF_PCR1x

value: F

value: NRSF

value: David Anderson, Caltech

value: one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12878_TCF3_(SC-349)_PCR1x

value: ChipSeq

value: Chromatin IP Sequencing

value: E2A.E12(V-18) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of E2A.E12 of human origin. Recommended for detection of E12 and E47 of m, r and h origin by WB, IP, IF, IHC(P), ELISA and indirect FCM using PE (sc-3739)- or FITC (sc-2012)-conjugated goat anti-rabbit IgG. Antibody Target:TCF3

value: Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs:5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer.

value: Santa Cruz Biotechnology


title: HudsonAlpha_ChipSeq_H1-hESC_ATF2_(SC-81188)_v042211.1

growth_protocol: missing

value: Mouse monoclonal IgG, raised against a recombinant protein corresponding to an internal region of ATF2 of human origin. Antibody Target:ATF2

value: This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq)


title: HudsonAlpha_ChipSeq_H1-hESC_SP4_(V-20)_v042211.1

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Sp4 of human origin. Antibody Target:SP4

value: Binds to GT and GC boxes promoters elements. Probable transcriptional activator.

value: MACS


title: HudsonAlpha_ChipSeq_SK-N-SH_GATA3_(SC-268)_v042211.1

source_name: SK-N-SH

value: Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target:GATA3

value: This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq).

value: Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target: GATA3


title: HudsonAlpha_ChipSeq_HUVEC_RevXlinkChromatin_PCR1x

source_name: HUVEC

tag: cell

value: HUVEC

tag: cell organism

value: human

tag: cell description

value: umbilical vein endothelial cells

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: U

value: RevXlinkChromatin

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_HepG2_MBD4_(SC-271530)_v042211.1

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Mouse monoclonal IgG, specific for an epitope mapping between a.a. 515-555 within an internal region of MBD4 of mouse origin. Antibody Target:MBD4

tag: antibody targetdescription

value: MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotechnology

value: M

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)


title: HudsonAlpha_ChipSeq_HL-60_NRSF_v042211.1

value: Mouse monoclonal. Antibody Target:NRSF

value: Neuron-restrictive silencer transcription factor

value: Dr. David Anderson at Caltech

tag: antibody vendorid

value: (Made by Protein Expression Center:pec@caltech.edu)

tag: controlid

tag: labexpid

tag: softwareversion

value: MACS

tag: cell sex

value: F

value: NRSF

value: David Anderson, Caltech


title: HudsonAlpha_ChipSeq_GM12878_Egr-1_PCR2x

value: Rabbit polyclonal, EGR-1 (588). Antibody Target:EGR1

value: Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner.

tag: antibody

tag: treatment

tag: treatment description

tag: protocol

tag: protocol description

value: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)


title: HudsonAlpha_ChipSeq_MCF-7_CTCF_(SC-5916)_v042211.1

value: ChipSeq

value: Chromatin IP Sequencing

value: Goat polyclonal IgG, epitope mapping at the N-terminus of CTCF of human origin. Antibody Target:CTCF

value: This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)

value: No special treatment or protocol applies

tag: replicate


title: HudsonAlpha_ChipSeq_ECC-1_TAF1_v042211.1

value: Mouse monoclonal (p250). Antibody Target:TAF1

value: TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.

value: Santa Cruz Biotechnology

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)


title: HudsonAlpha_ChipSeq_GM12878_MTA3_(SC-81325)_v042211.1

value: Mouse monoclonal IgG, raised against a recombinant protein corresponding to a region near the N-terminus of MTA3 of human origin. Antibody Target:MTA3

value: Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels.


title: HudsonAlpha_ChipSeq_A549_FOSL2_EtOH_0.02pct_v042211.1

value: Rabbit polyclonal. Fra-2(Q-20) is an affinity purified raised against the N-terminus of Fra-2 of human origin. Recommended for detection of Fra-2 of m, r, h and chicken origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:FOSL2

value: The Fos gene family consists of 4 members:FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation.

value: MACS

value: M

value: Fra-2(Q-20) is an affinity purified rabbit polyclonal raised against the N-terminus of Fra-2 of human origin. Recommended for detection of Fra-2 of m, r, h and chicken origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:FOSL2

value: 1 h with 0.02% Ethanol (Myers)


title: HudsonAlpha_ChipSeq_SK-N-SH_NRSF_v041610.1

value: ChipSeq

value: Mouse monoclonal. Antibody Target:NRSF

value: Neuron-restrictive silencer transcription factor

value: Dr. David Anderson at Caltech

value: (Made by Protein Expression Center:pec@caltech.edu)

value: F

value: NRSF

value: David Anderson, Caltech

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_A549_Max_v042211.1

value: Chromatin IP Sequencing

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target:Max

value: The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq).

value: Santa Cruz Biotechnology

value: Max

value: No special treatment or protocol applies

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)


title: HudsonAlpha_ChipSeq_A549_GATA3_(SC-268)_v042211.1

value: Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target:GATA3

value: This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq).

value: MACS

value: M

value: Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target: GATA3


title: HudsonAlpha_ChipSeq_GM12878_FOXM1_(SC-502)_v042211.1

value: ChipSeq

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of FOXM1 of human origin. Antibody Target:FOXM1

value: The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011)


title: HudsonAlpha_ChipSeq_MCF-7_ELF1_(SC-631)_v042211.1

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin. Antibody Target:ELF1

value: This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq)

value: F

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin. Antibody Target: ELF1


title: HudsonAlpha_ChipSeq_HL-60_Pol2-4H8_v042211.1

value: Chromatin IP Sequencing

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL2

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

value: abcam


title: HudsonAlpha_ChipSeq_K562_CBX3_(SC-101004)_v042211.1

value: Mouse monoclonal IgG, raised against recombinant CBX3 of human origin. Antibody Target:CBX3

value: At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.

value: Santa Cruz Biotechnology

value: No special treatment or protocol applies

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)


title: SNAPC4

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
alignment: BOWTIE v 0.12.7 (default parameters)
tag density files: genomeCoverageBed (from BEDTools suite)
Genome_build: hg 18
Supplementary_files_format_and_content: bedGraph: Tag density profiles

extract_protocol: ChIP-Seq DNA Sample Prep Kit (Illumina, inc.)

tag: cell line

value: non-tumorigenic epithelial cell line MCF 10A

tag: chip antibody

value: anti-SNAPC 190 (SNAAD17A) mouse monoclonal (Santa Cruz, sc-81379)


title: HudsonAlpha_ChipSeq_A549_JunD_EtOH_0.02pct_v041610.2

tag: datatype

value: ChipSeq

tag: datatype description

value: rabbit polyclonal IgG. Antibody Target:JunD

value: The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq)

value: MACS

value: M

value: JunD

value: 1 h with 0.02% Ethanol (Myers)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_SK-N-SH_GABP_v042211.1

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target:GABP

tag: antibody targetdescription

value: The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.

value: F

value: GABP


title: HudsonAlpha_ChipSeq_A549_FOXA2_(SC-6554)_EtOH_0.02pct_v041610.2

value: Goat polyclonal IgG, epitope mapping at the N-terminus of FOXA2 of human origin. Antibody Target:FOXA2

value: The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid


title: AGO1-DAH IP small RNA rep1

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: Small RNA isolated from immunoprecipitation of mutant HA-AGO1-DAH

library_source: transcriptomic

data_processing:
Sequencing reads from small RNA libraries were computationally processed to remove 3’ adaptor sequences, and sequences were consolidated to generate read counts per unique small RNA. Unique small RNAs were mapped to the A. thaliana genome (TAIR10) using Bowtie v0.12.8 (Langmead et al., Genome Biology 2009) with settings allowing for perfect matches only (bowtie –f –v 0 –a –S –p 10). Libraries were normalized for sequencing depth differences by randomly sampling genome-mapped small RNA read counts from each library to match the proportion of mapped reads from the smallest library, relative to the larger libraries, resulting in ~20 million reads per sample.
Genome_build: Arabidopsis thaliana Chr1-5, TAIR version 10
Supplementary_files_format_and_content: GFF (version 3) files are provided that contain small RNA mapping data and read abundances for the normalized datasets used in our study. GFF formats are specified in the header of each file.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: flowers stage 1-12

extract_protocol: Ten μl (or 100%) of the immunoprecipitated RNA was mixed with 15 pmol of Cloning Linker 1 (IDT), and incubated at 70ºC for 2 min. The mixture was cooled on ice for 2 min before adding 1.5 µl of 10X T4 RNA Ligase Reaction Buffer (NEB), 40 units of RNaseOUT (Invitrogen) and 10 units of T4 RNA Ligase 2 truncated K227Q (NEB). Ligation reactions were incubated overnight at 16ºC. Digestion of unligated Cloning Linker 1 was done by first adding 20 units of deadenylase (NEB) to the overnight ligation, and incubating at 30ºC for 15 min, then adding 10 units of Exonuclease VII (Affymetrix), and incubating at 37ºC for 15 min. Next, 15 pmol of RNA 5' adapter (GUUCAGAGUUCUACAGUCCGACGAUC) was denatured at 70ºC for 2 min followed by transfer to ice for at least 2 min. Denatured RNA 5’ adapter was added to the ligation mixture with 0.48 mM of ATP and 5 units of T4 RNA Ligase 1 (Ambion), and the resulting mixture was incubated at 28ºC for 1 h, then placed on ice. For cDNA synthesis, 5 µM of RT-Primer (ATTGATGGTGCCTACAG) was used with the SuperScript III First-Strand Synthesis System (Invitrogen). After cooling the cDNA synthesis reactions on ice, 2 units of E. coli RNase H (Invitrogen) were added, and the reaction was incubated at 37ºC for 20 min. Linear PCR reactions were done with half of the cDNA and in the presence of 1x Phusion HF Buffer, 0.25 µM of P5 primer (AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA), 0.25 µM of P7-modban (CAAGCAGAAGACGGCATACGAATTGATGGTGCCTACAG), 0.1 mM dNTP mix and 1 unit of Phusion Polymerase (Thermo Scientific). The following PCR conditions were used: 98ºC for 30 sec, 17 cycles of 98ºC for 10 sec, 60ºC for 30 sec, 72ºC for 15 sec; 72ºC for 5 min. The Qiagen PCR Purification Kit was used to clean up the PCR products before loading samples onto a 6% native polyacrylamide gel. The desired amplicons (between ~100-108 bp) were recovered from the gel using electro-transfer onto DE81 paper as previously described (Fahlgren et al., RNA 2009). DNA concentrations were quantified using the Qubit HS Assay Kit (Invitrogen) and submitted for sequencing on a HiSeq 2000 sequencer (Illumina).

tag: genetic background

value: Columbia

tag: transgene

tag: molecule

value: small RNA

tag: sample type

value: AGO1-DAH IP

tag: tissue

value: flower

tag: developmental stage

value: stages 1-12


title: IgG

value: non-tumorigenic epithelial cell line MCF 10A

value: normal rabbit IgG (Santa Cruz, sc2027)


title: HudsonAlpha_ChipSeq_A549_CREB1_(SC-240)_EtOH_0.02pct_PCR1x

value: ChipSeq

value: Mouse monoclonal IgG1; raised against amino acids 254-327 mapping within the DNA binding and dimerization domain of human CREB-1. Antibody Target:CREB1

value: This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq)

tag: controlid

tag: labexpid

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: antibody

tag: treatment

tag: treatment description

value: 1 h with 0.02% Ethanol (Myers)

tag: protocol

value: one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_T-47D_JunD_v042211.1

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: rabbit polyclonal IgG. Antibody Target:JunD

tag: antibody targetdescription

value: The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq)

tag: softwareversion

value: MACS

value: JunD

value: No special treatment or protocol applies

tag: protocol description

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)

tag: replicate


title: HudsonAlpha_ChipSeq_A549_CREB1_(SC-240)_EtOH_0.02pct_v041610.2

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

value: This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway.  Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_A549_CREB1_(SC-240)_DEX_100nM_v041610.2

value: ChipSeq

tag: controlid

value: 1 h with 100 nM Dexamethasone (Myers)


title: SNAPC1

tag: cell line

value: non-tumorigenic epithelial cell line MCF 10A

tag: chip antibody

value: anti-SNAPC1 rabbit polyclonal (SIGMA, S4950)


title: AGO1-DDH IP small RNA rep1

description: Small RNA isolated from immunoprecipitation of wild type HA-AGO1-DDH

tag: genetic background

value: Columbia

tag: transgene

tag: molecule

value: small RNA

tag: sample type

value: AGO1-DDH IP

tag: tissue

value: flower

tag: developmental stage

value: stages 1-12


title: RNAPII

value: anti-RNAPII N-20 rabbit polyclonal (Santa Cruz, sc899)


title: HudsonAlpha_ChipSeq_A549_FOXA1_(SC-101058)_EtOH_0.02pct_v041610.2

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: Mouse monoclonal IgG, raised against recombinant HNF-3a of human origin. Antibody Target:FOXA1

value: This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq)

tag: labexpid

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: antibody

value: Mouse monoclonal IgG, raised against recombinant HNF-3a of human origin. Antibody Target: FOXA1

tag: treatment

tag: treatment description

value: 1 h with 0.02% Ethanol (Myers)

tag: protocol


title: Vector IP small RNA rep1

description: Small RNA isolated from immunoprecipitation control

value: pMDC99-GUS (Vector)

value: Vector IP


title: NBL [MethylC-Seq]

city: Changchun

first: Mingyuan

last: Liu

state: Jilin

address: 5333 Xian Road

department: Institute of Zoonosis

country: China

institute: Jilin University

description: For NBL, there is no MR file, since there is no methylation regions (MR) detected.

data_processing:
Sequence alignment of MethylC-seq
Raw sequencing data were processed using the Illumina base-calling pipeline (Illumina Pipeline v1.3.1). Reads alignment, gene annotation and methylation level determination can be refered to the Methods section in the manuscript.
Briefly, the reads generated by Illumina sequencing were aligned onto the T.s reference genome. The Lambda genome was also included in the reference sequence as an extra chromosome so that reads originating from the unmethylated control DNA could be aligned. Because DNA methylation has strand specificity, the plus strand and the minus strand of the T.s genome were separated to form alignment target sequences. To do this, each cytosine in the genome was converted to a thymine, termed T-genome, which represented the plus strand. Meanwhile, each guanine in genome sequences was converted to adenosine, termed A-genome, which represented the minus strand. Additionally, the original forms of the reads were also transformed to deal with the BS-treatment nucleotide conversion in the alignment process. First, the observed cytosines on the forward read of each read pair were replaced in silico by thymines, and secondly, the observed guanines on the reverse read of each read pair were replaced in silico by adenosines. We then mapped the   alignment form   reads to the   alignment form   target sequence using SOAPaligner with default parameters. Every hit of a single placement with a minimum number of mismatches and a clear strand assignment was defined as an unambiguous alignment, and each alignment was used for mC ascertainment.
Identification of methylcytosines (mCs) and Methylation Regions (MRs) and determination of methylation level;  For mC identification, we transformed each aligned read and the two strands of the T.s genome back to their original forms to build an alignment. In the unique part of the genome, cytosines that were covered by cytosines from reads on the same strand or guanines from those on the opposite strand (hereafter, referred to as ascertainment bases) were called as potential methylated sites. To account for the inefficient conversion of the bisulfite treatment and for sequencing errors, a correction method based on binomial tests and false discovery rate constraints was applied to the data to build a high-quality methylome for each of the three stages. The probability p in the binomial distribution B(n,p) was estimated from the number of cytosine bases sequenced in reference cytosine positions in the unmethylated Lambda genome (referred to as the error rate: non-conversion plus sequencing error frequency). The bisulfite conversion rates for all samples were over 99%, and the error rates were as follows: Ad, 0.0060; ML, 0.0064; NBL, 0.0025. Then the mCs from the binomial distribution analysis were selected for determination of Methylation regions (MRs), which were defined as being under a threshold of more than 5 continuous methylated cytosines (either CpG or non-CpGs in at least one strand) and having a distance between adjacent mCs of less than the median value (18 bp) of all distance values. Stage-specific MRs were defined as containing more than 5 continuous mCs and no overlap between two samples.
Percentage methylation was computed as the fraction of reads number of   C   in the total reads number of  C  and T for each covered CpG site, and herein average percentage methylation of all cytosine residues for any genomic region covered therein. Density methylation (mC/C) was determined as the number of mCs divided by total number of C sites in any genomic region.
Genome_build: Trichinella spiralis-3.7.1
Supplementary_files_format_and_content: c2t.-pe.sop.gz file type shows pair-end mapped to the reference that was observed guanines on the reverse read of each read pair were in silico replaced by adenosines.
Supplementary_files_format_and_content: c2t.+pe.sop.gz file type shows pair-end mapped to the reference that was observed cytosines on the forward read of each read pair were in silico replaced by thymines.
Supplementary_files_format_and_content: c2t.-se.sop.gz file type shows single-end mapped to the reference that was observed guanines on the reverse read of each read pair were in silico replaced by adenosines.
Supplementary_files_format_and_content: c2t.+se.sop.gz file type shows single-end mapped to the reference that was observed cytosines on the forward read of each read pair were in silico replaced by thymines.
Supplementary_files_format_and_content: sop file format: 1.read ID, 2.read sequemce , 3.quality value of base, 4.time of mapped different place, 5.read source (-a file or -b file), 6.mapped read length, 7.the plus or minus of reference, 8.reference ID, 9.mapped start site, 10.mismatch number, 11.mismatch information
Supplementary_files_format_and_content: cout file format: 1.chromosome number, 2.C site position, 3.plus or minus chain, 4.C type, 5.basic C type, 6.copy number, 7.the number of methylated reads, 8.the number of non-methylated reads, 9.bernoulli distribution e-value
Supplementary_files_format_and_content: MR file format: 1.chromosome number, 2.start site, 3.end site

organism: Trichinella spiralis

source_name: newborn larvae

growth_protocol: Infective T.s muscle larvae were obtained from infected mice at 35 days post infection (dpi) by digestion of minced skeletal muscle in 1% pepsin and 1% HCl for 45 min at 42°C with agitation.Seventy male 6-week-old Wistar rats were then orally inoculated with a dose of 8000 infective muscle larvae. Adult worms (Ad1) were obtained from the intestine of ten rats at 30 h post infection. The remaining sixty rats were sacrificed at 6 dpi, and the adult worms (Ad6) were recovered and incubated in IMDM in 75-cm2 cell culture plates at 37°C.Newborn larvae were harvested every 6 h.

extract_protocol:
Prior to library construction, 5 µg of genomic DNA spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI) was fragmented using a Covarias sonication system to a mean size of approximately 200 bp. After fragmentation, libraries were constructed according to the Illumina Pair-End protocol with some modifications. Briefly, purified randomly fragmented DNA was subsequently treated with a mix of T4 DNA polymerase, Klenow fragment and T4 polynucleotide kinase to repair, blunt and phosphorylate the ends. The blunt DNA fragments were subsequently 3’ adenylated using Klenow fragment (3’-5’ exo-), followed by ligation to adaptors synthesised with 5’-methylcytosine instead of cytosine using T4 DNA Ligase. After each step, DNA was purified using the QIAquick PCR purification kit (Qiagen). After that, ZYMO EZ DNA Methylation-Gold Kit™ was employed to convert unmethylated cytosine into uracil, according to the manufacturer’s instructions, and 220-250 bp converted products were size selected. Finally, PCR was carried out in a final reaction volume of 50 µl, consisting of 20 µl of size selected fractions, 4 µl of 2.5 mM dNTP, 5 µl of 10× buffer, 0.5 µl of JumpStart™ Taq DNA Polymerase, 2 µl of PCR primers and 18.5 µl water. The thermal cycling program was 94°C for 1 min, 10 cycles of 94 °C for 10 s, 62°C for 30 s, 72°C for 30 s, and then a 5 min incubation at 72°C, before holding the products at 12°C. The PCR products were purified using the QIAquick gel extraction kit (Qiagen). Before analysis with Illumina Hiseq2000, the purified products were analysed by the Bioanalyser analysis system (Agilent, Santa Clara, USA) and quantified by real time PCR. Raw sequencing data were processed using the Illumina base-calling pipeline (Illumina Pipeline v1.3.1). The sodium bisulfite non-conversion rate was calculated as the percentage of cytosines sequenced at cytosine reference positions in the Lambda genome.
library strategy: MethylC-Seq

value: newborn larvae


title: AGO1-DAH INPUT transcript rep1

description: Transcript RNA isolated from immunoprecipitation of mutant HA-AGO1-DAH

data_processing:
Sequencing reads from transcript libraries were consolidated to generate read counts per unique sequence, and unique sequences were mapped to A. thaliana transcripts (TAIR10) using Bowtie (Langmead et al., Genome Biology 2009) with settings allowing for perfect matches only (bowtie –f –v 0 –a –S –p 10). Aligned sequences were filtered to remove reads that mapped to rRNA, tRNA, snRNA, snoRNA, and transposable elements, and to remove reads that mapped to transcripts from multiple genes or were derived from the transcript antisense strand. Libraries were normalized for sequencing depth differences by randomly sampling transcript-mapped read counts from each library to match the proportion of mapped reads from the smallest library, resulting in ~1 million reads per sample.
Genome_build: Arabidopsis thaliana gene models, TAIR version 10
Supplementary_files_format_and_content: GFF (version 3) files are provided that contain RNA fragment mapping data and read abundances for the normalized datasets used in our study. GFF formats are specified in the header of each file.

extract_protocol: Ten µg of total RNA or 10 μl (100%) of the immunoprecipitated RNA were treated with TURBO DNase I DNA-free (Ambion). Samples were depleted of ribosomal RNAs by treatment with Ribominus Plant Kit for RNA-Seq (Invitrogen) according to manufacturer’s instructions. cDNA synthesis and strand-specific target transcript libraries from both input RNA and immunoprecipitated RNA were made as described (Wang et al., PLoS ONE 2011), with the following modifications. Immunoprecipitated RNAs were not fragmented with metal ions prior to library construction, and 16 cycles were used in the linear PCR reaction. DNA adaptors 1 and 2 were annealed to generate the Y-shape adaptors, and oligonucleotides PE-F (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and PE-R (CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT) were used in the linear PCR. DNA amplicons were analyzed with a Bioanalyzer (DNA HS kit, Agilent), quantified using the Qubit HS Assay Kit (Invitrogen) and sequenced on a HiSeq 2000 sequencer (Illumina).

value: ribosome-depleted RNA

value: AGO1-DAH INPUT


title: AGO1-DDH INPUT transcript rep2

description: Transcript RNA isolated from immunoprecipitation of wild type HA-AGO1-DDH

value: Columbia

value: AGO1-DDH INPUT


title: Ad [MethylC-Seq]

source_name: adults

value: adults


title: HudsonAlpha_ChipSeq_K562_PML_(SC-71910)_v042211.1

value: ChipSeq

tag: antibody antibodydescription

value: Mouse monoclonal IgG, N-terminal epitope corresponding to residues 37-51 of PML of human origin. Antibody Target:PML

tag: antibody targetdescription

value: The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: controlid

tag: softwareversion

value: MACS

value: F

value: No special treatment or protocol applies

tag: protocol description

value: Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)

tag: replicate


title: AGO1-DAH INPUT transcript rep2

tag: genetic background

tag: transgene

tag: molecule

tag: sample type

tag: tissue

value: flower

tag: developmental stage

value: stages 1-12


title: ML [MethylC-Seq]

source_name: muscle larvae

value: muscle larvae


title: AGO1-DDH INPUT transcript rep1


title: AGO1-DDH IP transcript rep2

value: AGO1-DDH IP


title: AGO1-DAH IP transcript rep1

value: ribosome-depleted RNA

value: AGO1-DAH IP


title: AGO1-DAH IP transcript rep2

value: Columbia


title: Treg Foxp3 ChIP Rep1 (Tech Rep1)

city: New York

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

description: Treg Foxp3 ChIP Rep1 (Tech rep 1). File with peaks from combined replicates is linked to GSE40684.

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

organism: Mus musculus

source_name: Treg Foxp3 ChIP

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

treatment_protocol: Foxp3 antibody; custom polyclonal antibody that has been affinity purified

tag: cell type

value: Foxp3-positive CD4+ T cells

tag: cell source

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


title: Treg Input Rep1

description: Input Control Rep1

source_name: Treg Input


title: Treg Cbfb ChIP

description: Treg Cbfb ChIP

source_name: Treg Cbfb ChIP

treatment_protocol: Cbfb antibody; Santa Cruz Biotechnologies PEBP2beta (FL-182)  sc-20693-X Lot# D1003


title: CD4 Ets1 ChIP

description: CD4 Ets1 ChIP

source_name: CD4 Ets1 ChIP

treatment_protocol: Ets1 antibody; Santa Cruz Biotechnologies sc-350-X Lot# J1309

value: CD4+ Foxp3-negative T cells


title: CD4 Cbfb ChIP

description: CD4 Cbfb ChIP. Low quality sample has no processed data.

source_name: CD4 Cbfb ChIP


title: Treg Input Rep2

description: Input Control Rep 2


title: Treg Foxp3 ChIP Rep1 (Tech Rep2)

description: Treg Foxp3 ChIP Rep1 (Tech Rep 2). File with peaks from combined replicates is linked to GSE40684.


title: Treg Ets1 ChIP

description: Treg Ets1 ChIP

source_name: Treg Ets1 ChIP


title: Treg Foxp3 ChIP Rep2

description: Treg Foxp3 ChIP Rep 2. File with peaks from combined replicates is linked to GSE40684.


title: HudsonAlpha_ChipSeq_GM12878_STAT5A_(SC-74442)_v042211.1

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Mouse monoclonal IgG, recommended for the detection of Stat5a and Stat5b of human origin by WB, IP, IF and ELISA. Antibody Target:STAT5A

value: The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq)

tag: labexpid

tag: cell sex

tag: antibody

tag: treatment

tag: treatment description

tag: protocol


title: T14_IgG_ChIPSeq

status: Public on Sep 27 2012

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
ChIP-seq reads were aligned to the mm8 genome assembly using Bowtie (0.12.7) independently for each lanes, with a setting to discard reads that are mapped to multiple genomic positions (m = 1). For reads that are mapped to same position, only one copy was retained.
Genome_build: mm8

source_name: Resting T cells, conconavalin A (conA) activation for 14hrs

growth_protocol: Isolated splenocytes were cultured at 0.5-1 X 106 cells /ml in 37oC and 5% of CO2 incubator with RPMI 1640 (Gibco-Invitrogen) in the presence of Hepes, L-glutamine, sodium pyruvate and 50mM β-mercaptoethanol (SIGMA).

extract_protocol: Library construction for ChIP-Seq follows the protocols as described in (PMID: 17512414)

treatment_protocol: B-splenocytes were treated with 25ug/ml of LPS for 0-4hrs.  The T-cells were treated with 7.5ug/ml of ConA for 0, 4 or 14 hrs, respectively.

value: spleen

value: Resting T cells

value: Santa Cruz SC-2025


title: T4_IgG_ChIPSeq

source_name: Resting T cells, conconavalin A (conA) activation for 4hrs


title: CD4 Elf1 ChIP

description: CD4 Elf1 ChIP

source_name: CD4 Elf1 ChIP

treatment_protocol: Elf1 antibody; Santa Cruz Biotechnologies sc-631-X Lot# G2406


title: B4_IgG_10058_ChIPSeq_2

source_name: Quiescent B cells, lipopolysaccharide (LPS) and 10058-F4 treatments for 4hrs

value: Quiescent B cells


title: Treg Elf1 ChIP

description: Treg Elf1 ChIP

source_name: Treg Elf1 ChIP


title: T4_Myc_ChIPSeq

value: Clontech, 632460


title: B4_Myc_10058_ChIPSeq


title: T14_Myc_ChIPSeq


title: B4_IgG_10058_ChIPSeq_1


title: B4_Pol2_10058_ChIPSeq

value: Abcam, ab5408


title: AGO1-DDH IP transcript rep1

value: AGO1-DDH IP

value: flower

value: stages 1-12


title: B4_IgG_wt_ChIPSeq

source_name: Quiescent B cells, lipopolysaccharide (LPS) treatment for 4hrs


title: B0_Myc_ChIPSeq

source_name: Quiescent B cells


title: B4_Pol2_wt_ChIPSeq


title: B4_IgG_ChIPSeq


title: B0_IgG_ChIPSeq


title: B4_Myc_ChIPSeq


title: H3shutoff-RNA-3hr-rep2

status: Public on Sep 26 2012

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description: RNA isolation from wildtype cells after 3 hours in dextrose

data_processing: RNA-seq reads from three biological replicates each of H3 shutoff and wildtype cells were mapped to the S. cerevisiae sacCer1 genome using TopHat (v. 1.1.0) and Bowtie (v. 0.12.6.0) with a maximum intron size of 1 kb. Samtools (v. 0.1.8.0) was used to determine pileups at each base in the genome.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown with shaking at 30C in media containing 1% yeast extract, 2% peptone, 2% galactose and grown to an OD600 of between 0.8 and 1.

extract_protocol: RNA was isolated using the hot acidic phenol method (Xiao et al., 2003) from wildtype and H3-shutoff cells grown as previously described and transitioned to dextrose-containing media for 3 hours. RNA was cleaned up using the RNEasy Mini Kit (Qiagen 74104). Ribosomal RNA was removed using the RiboMinus system (Invitrogen K155003). Quality of RNA and absence of ribosomal RNA was confirmed by gel electrophoresis. 4.5ug of ribo-minus RNA was then fragmented at 70C for 5 minutes (Ambion AM8740) and used as input for double-strand cDNA synthesis using Invitrogen Double-Stranded cDNA synthesis kit (Invitrogen 11917-010) with random priming (Invitrogen 48190-011). The resulting cDNA was then prepared for Solexa sequencing using UNC HTSF protocol v. 2.5 for single-end, multiplex sequencing.

treatment_protocol: Cells were collected by filtration using a 0.2ul filter, washed with media containing 1% yeast extract, 2% peptone, 2% dextrose, and resuspended at the intial concentration in fresh media containing 1% yeast extract, 2% peptone, 2% dextrose.

tag: strain

tag: carbon source

value: dextrose

tag: time point

value: 3 hours

tag: od


title: H3shutoff-RNA-3hr-rep1


title: wild-type-RNA-3hr-rep2

description: RNA isolated following H3 depletion after 3 hours in dextrose


title: RNAPII-5p_ChIP-seq

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing: The sequence tags were mapped to the human genome (UCSC hg18) by using the Genome Analyzer data analysis pipeline. The mapped sequence reads were extended to the average size of fragment length (200bp).

source_name: NCCIT

extract_protocol: The purified ChIP DNA fragments were ligated to a pair of adaptors for sequencing on the Illumina Genome Analyzer. The ligation products were size-fractioned to obtain 200 to 300-bp fragments on an agarose gel and subjected to 18 cycles of PCR amplification. Cluster generation and 72 cycles of single-read sequencing was done.

treatment_protocol: NCCIT embryonic carcinoma cell lines on a 10cm dish were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% antibiotic-antimycotic solution (Hyclone) at 37ºC in a humidified atmosphere composed of 5% CO2.

value: embryonic carcinoma cell line

tag: cell line

value: NCCIT

value: RNAPII

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #

tag: antibody lot #

value: unknown


title: H3shutoff-RNA-3hr-rep3


title: hDot1L_ChIP-seq

tag: cell type


title: B4_IgG_ChIPSeq_rpt

tag: tissue


title: B4_Myc_ChIPSeq_rpt


title: wild-type-RNA-3hr-rep1


title: H3shutoff-MNase-3hr-rep4

description: MNase digestion of H3 shutoff cells after H3 depletion following 3 hours in dextrose

data_processing:
WIG files - Reads were aligned to the sacCer1 version of the yeast genome using Bowtie v. 0.12.6 with default settings, a minimum insert size of 100 bp and a maximum insert size of 200 bp. Reads aligning to the rDNA locus (chr12 450,000-472,5000) were removed and 5 million reads were randomly selected from the remaining, aligned reads to generate the final, selected reads for each experiment. If less than 5 million filtered reads remained from a sample, a second, technical replicate (resequencing of same DNA) was obtained and the two filtered run files were combined.
TXT files - A dyad density map was created for each experiment using the center of each mapped, selected read. The dyad density map was Gaussian smoothed with a s.d. of 10 bp and a window of 3 s.d. For each chromosome, the smoothed dyad density maximum was selected as the center of a nucleosome. The protected region for the nucleosome was calculated by averaging the fragment length of all reads covering the called nucleosomeâs dyad. The s.d. of the dyad was calculated using the raw dyad counts that fell within the nucleosomeâs protected region. All bases within 1 protected region of the nucleosome dyad were set to a smoothed dyad density of 0 and the process repeated until no remaining nucleosomes could be called. Nucleosome occupancy was defined as the number of read centers falling within a 100 bp window centered on the nucleosome dyad.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 minutes at room temperature with shaking. Crosslinking was quenched by addition of glycine to a final concentration of 0.125 M and incubation at room temperature for 5 minutes. Cells were then spun down at 3000 rpm in a Sorvall RT-34 centrifuge, washed twice with 20 mL of 1 M sorbitol, and resuspended in a final volume of 10 mL in spheroplast digestion buffer [1 M sorbitol, 1mM 2-mercaptoethanol (Fischer Scientific BP176100) and 42000 U of lyticase (Sigma-Aldrich L2524)]. Cells were rocked at 30Â°C for 15 minutes, spun down at 3000 rpm in a Sorvall RT-34 centrifuge, and washed twice with 10 mL of 1 M sorbitol. Spheroplasts were resuspended at 0.12 g spheroplast/mL of MNase digestion buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40 with 1 mM 2-mercaptoethanol and 0.5 mM spermidine added immediately before use). 600ul aliquots were digested with a titration of micrococcal nuclease A (Worthington-Biochemical LS004797) ranging from 0 to 50U for 15 minutes at 37C. Digestion was stopped with 150ul stop buffer (5% SDS, 50 mM EDTA). 5ul of a 20 mg/mL stock solution of Proteinase K (Roche 03 115 879 001) was added and the tube incubated at 65C overnight to reverse crosslinking. DNA was isolated by standard phenol:chloroform extraction (2x) and precipitated using isopropanol. DNA was dried and resuspended in 15ul of ddH2O.  1ul of  previously boiled 10 mg/mL RNase A (Sigma Aldrich R5503) was added and the reaction incubated at 37C for 30-60 minutes to digest RNA. The DNA was then loaded on a 2% agarose gel, run out, and the band corresponding to a mono-nucleosome band in the sample showing clear mono-, di- and tri-nucleosome bands gel extracted using a dark reader (Clare ChemicalResearch DR46B Transilluminator). Samples were prepared using UNC HTSF protocol v. 2.5 for paired-end, multiplex sequencing.

treatment_protocol: Cells were collected by filtration using a 0.2um filter, washed with media containing 1% yeast extract, 2% peptone, 2% dextrose, and resuspended at the intial concentration in fresh media containing 1% yeast extract, 2% peptone, 2% dextrose.

tag: fragment size (mean)

tag: fragment size (s.d.)


title: wildtype-MNase-0hr-rep1_C

description: MNase digestion of wildtype cells immediately after transition to dextrose

value: 0 hours


title: wildtype-MNase-3hr-rep1_B

description: MNase digestion of wildtype cells following 3 hours in dextrose


title: H3shutoff-MNase-0hr-rep3

description: MNase digestion of H3 shutoff cells immediately after transition to dextrose


title: H3shutoff-MNase-3hr-rep3


title: 46h hmC DIP-seq

city: Princeton

first: John

middle: Russell

last: Bracht

state: NJ

address: Washington Rd. Guyot Hall rm 323

institute: Princeton University

description: JRB310+JRB510 at 46hr postmixing

data_processing:
Mapping (with BWA) of raw data onto MAC Oxytricha genome, which is already fragmented into ~18,000 nanochromosomes, or a representative MIC genome consisting of 56 chromosomes (largely repetitive).
RPKM of each nanochromosome (or contig) computed for Vegetative and 46h samples
Subtract Vegetative RPKM from 46h RPKM: this number is the "signal" or excess reads at 46h. This data included in the two processed data files (one for MAC, one for MIC).
plot IgG signal vs mC or hmC signal, included in paper
Genome_build: v1.0
Supplementary_files_format_and_content: tab-deliminated columns: nanochromosome (contig) name <tab> IgG signal <tab> mC signal <tab> hmC signal

organism: Oxytricha trifallax

source_name: 46h hmC

growth_protocol: Standard Oxytricha culture in Pringsheim media

extract_protocol:
DNA extracted with the Machery Nagel NucleoSpin Tissue Kit
Followed standard DNA library construction but IP performed before PCR amplification step. Fragment the DNA, ligate adaptors. Vegetative and 46h libraries had different barcodes and were mixed together at this stage for IP. Material recovered by the antibody was subjected to 15 cycles of PCR and gel purified before submission to sequencing facility.

library_selection: hydroxymethylcytidine antibody

treatment_protocol: conjugation induced by mixing lightly starved cells and allowing conjugation to proceed to the 46h timepoint.

tag: Stage

value: conjugating cells

value: anti-hydroxymethylcytosine (Rabbit) Active Motif, CAT# 39791, lot# 13611004


title: H3shutoff-MNase-0hr-rep4


title: 46h mC DIP-seq

description: JRB310+JRB510 at 46hr postmixing

source_name: 46h mC

extract_protocol:
DNA extracted with the Machery Nagel NucleoSpin Tissue Kit
Followed standard DNA library construction but IP performed before PCR amplification step. Fragment the DNA, ligate adaptors. Vegetative and 46h libraries had different barcodes and were mixed together at this stage for IP. Material recovered by the antibody was subjected to 15 cycles of PCR and gel purified before submission to sequencing facility.

tag: antibody

value: anti-methylcytosine (mouse) Eurogentec, CAT# BI-MECY-0100


title: wildtype-MNase-0hr-rep1

data_processing:
WIG files - Reads were aligned to the sacCer1 version of the yeast genome using Bowtie v. 0.12.6 with default settings. Single end reads were extended to the average fragment size of the experiment. Reads aligning to the rDNA locus (chr12 450,000-472,5000) were removed and 5 million reads were randomly selected from the remaining, aligned reads to generate the final, selected reads for each experiment.
TXT files - A dyad density map was created for each experiment using the center of each mapped, selected read. The dyad density map was Gaussian smoothed with a s.d. of 10 bp and a window of 3 s.d. For each chromosome, the smoothed dyad density maximum was selected as the center of a nucleosome. The protected region for the nucleosome was calculated by averaging the fragment length of all reads covering the called nucleosomeâs dyad. The s.d. of the dyad was calculated using the raw dyad counts that fell within the nucleosomeâs protected region. All bases within 1 protected region of the nucleosome dyad were set to a smoothed dyad density of 0 and the process repeated until no remaining nucleosomes could be called. Nucleosome occupancy was defined as the number of read centers falling within a 100 bp window centered on the nucleosome dyad.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 minutes at room temperature with shaking. Crosslinking was quenched by addition of glycine to a final concentration of 0.125 M and incubation at room temperature for 5 minutes. Cells were then spun down at 3000 rpm in a Sorvall RT-34 centrifuge, washed twice with 20 mL of 1 M sorbitol, and resuspended in a final volume of 10 mL in spheroplast digestion buffer [1 M sorbitol, 1mM 2-mercaptoethanol (Fischer Scientific BP176100) and 42000 U of lyticase (Sigma-Aldrich L2524)]. Cells were rocked at 30C for 15 minutes, spun down at 3000 rpm in a Sorvall RT-34 centrifuge, and washed twice with 10 mL of 1 M sorbitol. Spheroplasts were resuspended at 0.12 g spheroplast/mL of MNase digestion buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40 with 1 mM 2-mercaptoethanol and 0.5 mM spermidine added immediately before use). 600ul aliquots were digested witha titration of micrococcal nuclease A (Worthington-Biochemical LS004797) ranging from 0 to 50U for 15 minutes at 37C. Digestion was stopped with 150ul stop buffer (5% SDS, 50 mM EDTA). 5ul of a 20 mg/mL stock solution of Proteinase K (Roche 03 115 879 001) was added and the tube incubated at 65C overnight to reverse crosslinking. DNA was isolated by standard phenol:chloroform extraction (2x) and precipitated using isopropanol. DNA was dried and resuspended in 15ul of ddH2O. 1ul of previously boiled 10 mg/mL RNase A (Sigma Aldrich R5503) was added and the reaction incubated at 37C for 30-60 minutes to digest RNA. The DNA was then loaded on a 2% agarose gel, run out, and the band corresponding to a mono-nucleosome band in the sample showing clear mono-, di- and tri-nucleosome bands gel extracted using a dark reader (Clare ChemicalResearch DR46B Transilluminator). Samples were prepared using a modified version of the Illumina Solexa preparation protocol. DNA was blunted using the END-IT DNA Repair Kit (Epicentre ER0720). 50 ng of mononucleosome DNA was incubated with 5ul 10x buffer, 5ul dNTP mix, 5ul ATP solution and 1ul enzyme mix in a 50ul reaction for 60 minutes at room temperature. DNA was recovered using the QIAQuick Gel Extraction kit (Qiagen 28704) with 50ul ddH2O and 400ul of QG buffer. DNA was eluted using 2 15ul elutions and then adenylated using 1ul of NEB exo- klenow (M212M), 5ul Klenow buffer and 1ul 10mM dATP in a 50ul reaction for 60 minutes at room temperature. DNA was isolated using a QIAquick MinElute kit (Qiagen 28006) and eluted in 10ul of EB. Adapters were ligated using NEB Quick T4 DNA Ligase (M2200S) with a 10:1 dilution of adapters provided by the UNC High Throughput Sequencing Facility (UNC HTSF) in a 50ul reaction containing 10ul of DNA, 25ul 2X Quick Ligation Buffer, 2uL adapters and 1ul DNA ligas for 25 minutes at room temperature. DNA was purified using a QIAQuick MinElute column and eluted in 10ul of EB. DNA was amplified using Stratagene PfuUltra II Fusion HS DNA Polymerase (Stratagene 600670) using 2ul DNA, 2ul Solexa single-end PCR primers, 10ul 10X PfuUltra II buffer, 10ul 2.5 mM dNTP and 1ul of Pfu Ultra II DNA polymerase in a 100uL reaction with the following cycling conditions: 95C for 1 minute; 18 cycles of 95C for 50 seconds, 65C for 60 seconds, 72C for 30 seconds; 72C for 5 minutes; 4C hold. DNA was purified using the QIAQuick MinElute kit in 10ul of buffer EB and run out on a 2% agarose gel. The band corresponding to mononucleosome + adapters (approximately 250 base pairs) was cut out on the dark reader, gel extracted using the QIAQuick Gel Extraction kit, and submitted to UNC HTSF for sequencing.


title: H3shutoff-MNase-3hr-rep2


title: wildtype-MNase-3hr-rep1_C


title: 46h IgG DIP-seq

description: JRB310+JRB510 at 46hr postmixing

source_name: 46h IgG

extract_protocol:
DNA extracted with the Machery Nagel NucleoSpin Tissue Kit
Followed standard DNA library construction but IP performed before PCR amplification step. Fragment the DNA, ligate adaptors. Vegetative and 46h libraries had different barcodes and were mixed together at this stage for IP. Material recovered by the antibody was subjected to 15 cycles of PCR and gel purified before submission to sequencing facility.

library_selection: IgG antibody

value: anti-IgG (mouse) Santa Cruz Biotechnology, CAT# sc-2025, lot C1111


title: wildtype-MNase-0hr-rep1_B


title: wildtype-MNase-3hr-rep1


title: Vegetative hmC DIP-seq

description: JRB310+JRB510 DNA, mixed 1:1

source_name: Vegetative hmC

value: vegetative cells


title: H3shutoff-MNase-0hr-rep2


title: H3shutoff-MNase-0hr-rep1


title: Vegetative IgG DIP-seq

description: JRB310+JRB510 DNA, mixed 1:1

source_name: Vegetative IgG


title: wild-type-RNA-3hr-rep3


title: Vegetative mC DIP-seq

description: JRB310+JRB510 DNA, mixed 1:1

source_name: Vegetative mC


title: Duke_DnaseSeq_Urothelia_UT189

status: Public on Sep 25 2012

source_name: Urothelia

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: labversion

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

tag: replicate

tag: cell

value: Urothelia

tag: cell organism

value: human

tag: cell description

value: primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene

tag: cell karyotype

value: normal

tag: cell sex

value: F

tag: treatment

value: UT189 E.Coli treatment 1 hour, followed by 24 hour incubation

value: baseAlignCounts.pl v 1


title: GIS_RnaPet_GM12878_cytosol_longPolyA

molecule: polyA RNA

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaPet

tag: lab

value: GIS

tag: lab description

value: Ruan - Genome Institute of Singapore

value: RnaPet

value: RNA Paired-End Tag

value: lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell lineage

value: mesoderm

tag: localization

value: cytosol

tag: localization description

value: The fluid between the cells outer membrane and the nucleus

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

value: clone-free

tag: replicate description

value: tier 1


title: Duke_DnaseSeq_Adult_CD4_Th1

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

tag: replicate

value: human

value: CD4+ cells isolated from human blood and enriched for Th1 populations

value: B


title: Duke_DnaseSeq_Urothelia

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

tag: cell

value: Urothelia

tag: cell organism

tag: cell description

value: primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene

tag: cell karyotype

value: normal

value: F

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_H7-hESC

value: undifferentiated embryonic stem cells

value: inner cell mass

tag: cell sex

value: U


title: Duke_DnaseSeq_K562_NaBut

treatment_protocol: NaBut

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_K562

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: cancer

tag: cell lineage

value: mesoderm

tag: treatment

value: NaBut

tag: treatment description

value: 0.5 mM Sodium Butyrate for 72 hours


title: Duke_DnaseSeq_GM13976

value: DnaseSeq

value: DNaseI HS Sequencing

value: human

value: lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977


title: Duke_DnaseSeq_iPS_NIHi7

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: iPS cells derived from AG08395 fibroblast


title: Duke_DnaseSeq_Olf_neurosphere

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: Human olfactory neurosphere-derived cells from mucosal biopsies

value: normal


title: Duke_DnaseSeq_RWPE1

value: prostate epithelial

value: M

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_IMR90

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: endoderm

value: F


title: Duke_DnaseSeq_Monocytes-CD14+

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_CD14_monocytes

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2:not in 2011 analysis

value: mesoderm


title: H3shutoff-MNase-3hr-rep1

tag: strain

tag: carbon source

value: dextrose

tag: time point

value: 3 hours

tag: od


title: Duke_DnaseSeq_MCF-7_CTCF_shRNA_knockdown

value: DnaseSeq

value: DNaseI HS Sequencing

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

value: human

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: cancer

value: ectoderm

value: CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct.


title: Duke_DnaseSeq_GM10266

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12)

value: affected

value: M

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_ECC-1_DMSO_0.02pct

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

value: endoderm

value: F

value: 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)


title: Duke_DnaseSeq_CD20+_RO01794

value: DnaseSeq

value: DNaseI HS Sequencing

value: B cells, African American, draw number 1, newly promoted to tier 2:not in 2011 analysis

value: normal

value: mesoderm


title: Duke_DnaseSeq_GM10248

value: human

value: lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12)


title: Duke_DnaseSeq_GM20000

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation


title: Duke_DnaseSeq_Cerebellum_OC

value: Primary frozen cerebellum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian


title: Duke_DnaseSeq_GC_B_cell

value: Germinal center B cells (CD77+) isolated from de-identified tonsillectomy

value: U


title: Duke_DnaseSeq_Cerebrum_frontal_OC

value: Primary frozen frontal cerebrum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian

value: M

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_SK-N-SH

source_name: SK-N-SH

value: immortalized cell line

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

tag: line

value: SK-N-SH

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: cancer

value: ectoderm

value: F


title: Duke_DnaseSeq_Ishikawa_4OHTAM_100nM_30m

source_name: Ishikawa

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

value: Ishikawa

value: human

value: endometrial adenocarcinoma

value: 30 minutes with 100 nM 4-hydroxytamoxifen (Crawford)


title: Duke_DnaseSeq_K562_SAHA_ctrl

tag: datatype description

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_K562

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: mesoderm

value: Cells grown with DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (DMSO volume is ~ .05% of the total media volume). This is an untreated control.


title: Duke_DnaseSeq_K562_G1_phase

tag: labversion

value: Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of the single DNA content peak taken as G1 cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford)

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_MCF-7_Randomized_shRNA_control

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

tag: replicate

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct.


title: Duke_DnaseSeq_Medullo_D341

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

tag: cell

value: Medulloblastoma cell line of neuron or neuron precurosr origin

value: cancer

value: U


title: Duke_DnaseSeq_T-47D_Estradiol_10nM_30m

value: DnaseSeq

value: DNaseI HS Sequencing

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

tag: cell organism

value: epithelial cell line derived from a mammary ductal carcinoma.

value: F

value: 30 min with 10nM 7b-Estradiol (Crawford)


title: Duke_DnaseSeq_ECC-1_Estradiol_10nM_30m

value: human

tag: cell description

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

value: endoderm


title: Duke_DnaseSeq_FibroP_AG08395

value: fibroblasts taken from individuals with Parkinson's disease

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_HEK293T

value: embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line

value: mesoderm


title: Duke_DnaseSeq_Ishikawa_Estradiol_10nM_30m

value: Ishikawa

value: endometrial adenocarcinoma


title: Duke_DnaseSeq_Colo829

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: malignant melanoma

tag: cell karyotype

value: cancer

value: M


title: Duke_DnaseSeq_K562_G2-M_phase

value: DnaseSeq

value: DNaseI HS Sequencing

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_K562

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell sex

value: Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of double DNA content taken as G2 and M cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford)


title: Duke_DnaseSeq_iPS_NIHi11

value: human

value: iPS cells derived from AG20443 fibroblast


title: Duke_DnaseSeq_MCF-7_Hypoxia_LacAcid_ctrl

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell lineage

value: ectoderm

value: F

value: Untreated cells grown along side Hypoxia LacAcid treated cells (Crawford)


title: Duke_DnaseSeq_Fibrobl_GM03348_lenti-MyoD

treatment_protocol: lenti-MyoD

value: skin fibroblast

value: normal

tag: treatment

value: lenti-MyoD

value: GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were induced for MYOD expression for 10 days with doxycycline and at concentration of 3ug per ml. Standard media was used (and replaced every 2 days) during induction:DMEM, 1% Pen Strep, and 10% FBS. (Crawford)

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_Frontal_cortex_OC

value: DnaseSeq

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2)


title: 48hr_Pol2_ChipSeq

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against 48hr_Pol2

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embryonic stem cells

growth_protocol: Protocol H1 cells were grown to confluence in mTESR1 media. Cells were then differentiated for 48 hours in RPMI-B27 plus 50 ng/ml Activin

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Sample was divided into 6 aliquots after sonication. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

value: RNA Pol II (Rpb1 N-terminus)

tag: antibody vendor/catalog#

value: Santa Cruz SC-899X

tag: cell line


title: Duke_DnaseSeq_FibroP_AG08396

value: DNaseI HS Sequencing

value: human

value: fibroblasts taken from individuals with Parkinson's disease


title: 48hr_H3K27me3_ChipSeq

description: Chromatin IP against 48hr_H3K27me3

growth_protocol: H1 cells were grown to confluence in mTESR1 media. Cells were then differentiated for 48 hours in RPMI-B27 plus 50 ng/ml Activin

value: Abcam AB6002


title: Duke_DnaseSeq_FibroP_AG20443

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: M


title: Duke_DnaseSeq_Fibrobl_GM03348_lenti-control

treatment_protocol: lenti-control

value: lenti-control

tag: treatment description

value: GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were cultured for 10 days (NO DOXYCYCLINE) (Crawford)


title: Duke_DnaseSeq_iPS_CWRU1

value: iPS cells derived from MSC658 fibroblast


title: Duke_DnaseSeq_Psoas_muscle_OC

value: Primary frozen psoas muscle tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1540 (Rep B1), 1863 (Rep B2 FAIRE)

value: normal

value: B


title: Duke_DnaseSeq_Fibrobl_GM03348

value: DnaseSeq

value: skin fibroblast

value: baseAlignCounts.pl v 1


title: Duke_DnaseSeq_Heart_OC

value: Primary frozen heart tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B1 FAIRE), 4548 (Rep B2 FAIRE)


title: cMyc ChIPSeq H2171 rep2

description: Chromatin IP against cMyc in H2171 SCLC rep2

source_name: Small Cell Lung Carcinoma

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: cMyc

value: Santa Cruz SC-764


title: Max_ChIPSeq H2171 rep2

description: Chromatin IP against Max in H2171 SCLC rep2

value: Max

value: Santa Cruz SC-197


title: Max_ChIPSeq H128 rep2

description: Chromatin IP against Max in H128 SCLC rep2


title: WCE H128_2

description: WCE for H128 rep2


title: Duke_DnaseSeq_K562_SAHA_1uM_72hr

value: DNaseI HS Sequencing

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_K562

value: human

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: cancer

value: mesoderm

value: F

value: Cells grown with 1 uM suberoylanilide hydroxamic acid (SAHA) dissolved in DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (SAHA vehicle volume is ~ .05% of the total media volume). SAHA was provided by Cayman Chemical, item # 10009929.


title: Duke_DnaseSeq_Naive_B_cell

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: Naive B cells (IgD+) isolated from de-identified tonsillectomy

value: normal

value: U


title: WCE_H2171 rep2

description: WCE for H2171 SCLC rep2


title: Duke_DnaseSeq_Adult_CD4_Th0

value: DnaseSeq

value: CD4+ cells isolated from human blood and enriched for Th0 populations

value: B

value: baseAlignCounts.pl v 1


title: Rrp6 rep2

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

description: 5' barcode: NNNCGCTTAGC

data_processing:
Basecalls performed using Illumina CASAVA version 1.3, except for Sample 8 (Rrp44-endo rep2), which was analyzed with CASAVA version 1.8
CRAC reads were mapped to the sacCer2 genome with Novoalign, using the following settings: -F ILMFQ -aTGGAATTCTCGGGTGCCAAGG -r Random -h 150 -s (except Sample 8 for which -F STDFQ was used)
Genome_build: SacCer2 (SGD)
Supplementary_files_format_and_content: Mapped coordinates were converted to wig format using custom perl scripts

source_name: cells grown in SD (-URA/-TRP) medium

growth_protocol: Yeast cell cultures were grown in SD medium (OD600 ~0.5).

extract_protocol: Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol. Recovered RNAs are subjected to limited RNAse digest, linker ligation and cDNA amplification, and identified by Illumina sequencing (according to Granneman et al., PNAS, 2009).

treatment_protocol: To generate RNA-protein crosslinks, actively growing yeast cell cultures in SD medium were UV-irradiated in a 1.2 m metal tube (“Megatron”) for 100 sec at 254 nm (according to Granneman et al., EMBO J., 2011).

tag: strain

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0)

tag: tagged protein

value: Rrp6-HTP (genomic)


title: Rrp6 rep1

description: 5' barcode: none


title: 48hr_H3K79me2_ChipSeq

description: Chromatin IP against 48hr_H3K79me2

value: Abcam AB3594


title: Rrp44-N

description: 5' barcode: CACAGC

source_name: cells grown in SD (-LEU/-TRP) medium

value: MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0; rrp44-delta::kanMX6

value: Rrp44-WT-N-terminus, His6 - PP inserted at aa 241 + C-terminal TEV - protA (pRS315)


title: Rrp44-endo rep2

description: 5' barcode: none

value: Rrp44-endo-HTP (pRS315)


title: Rrp44 rep2

description: 5' barcode: NNNTAAGC

value: Rrp44-WT-HTP (pRS315)


title: Rrp44-C

description: 5' barcode: ACAAGC

value: Rrp44-WT-C-terminus, PP inserted at aa 241 + C-terminal His6 - TEV - protA (pRS315)


title: Rrp44-exo-C

description: 5' barcode: none

value: Rrp44-exo-C-terminus, PP inserted at aa 241 + C-terminal His6 - TEV - protA (pRS315)


title: Rrp44-exo rep2

description: 5' barcode: ACAAGC

value: Rrp44-exo-HTP (pRS315)


title: Rrp44 rep1

description: 5' barcode: none


title: Rrp44-exo rep1

description: 5' barcode: none


title: Csl4 rep2

description: 5' barcode: GA

value: Csl4-HTP (genomic)


title: Rrp44-endo rep1

description: 5' barcode: CACAGC


title: cMyc_ChIPSeq in H128 rep2

description: Chromatin IP against cMyc H128 SCLC rep2

value: cMyc

value: Santa Cruz SC-764


title: Csl4 rep1

description: 5' barcode: ACAAGC


title: Rrp44-exo-N

description: 5' barcode: none

value: Rrp44-exo-N-terminus; His6 - PP inserted at aa 241 + C-terminal TEV - protA  (pRS315)


title: Duke_DnaseSeq_GM13977

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: human

value: lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976

value: affected

value: mesoderm

value: F


title: ChIP seq H3K4me3 A95

status: Public on Sep 24 2012

city: Rehovot

first: Gilad

last: Landan

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

data_processing: MeDIP-seq: Uniquely mappable reads were extended to 180bp and raw coverage profiles for genomic bins of 50bp were obtained. Coverage trends were then generated for each condition by computing the distribution of MeDIP-seq coverage in groups of loci with a fixed range of CpG content (calculated in 800bp linearly-weighted windows, using bins of 0.5% CpG content). Coverage distributions were computed while excluding regions that were not uniquely mappable and regions that were identified as hypo-deaminated CpG islands. The 75th quantile of the coverage distributions for each condition were defined as master trends. Data from condition A95 was used as a reference master trend. Normalized methylation profiles were generated by multiplying raw coverage values for a 50bp genomic bin by the ratio between the condition and reference master trend at the appropriate CpG content bin. ChIP-seq: Uniquely mappable reads were extended to 180bp and raw coverage profiles for genomic bins of 50bp were obtained. Genome_build: hg18. Supplementary_files_format_and_content: 50bp-binned profiles were converted to BigWig format. To generate the bigwig files, 50bp resolution piled-up ChIP-seq and MeDIP-seq profiled were processed by the UCSC genome browser utility program.

source_name: WI-38 cell culture

growth_protocol: Cells were grown in MEM supplemented with 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine, and antibiotics. 100,000 cells were seeded in a 10cm plate during each weekly passaging.

extract_protocol: MeDIP-seq: 5ug of genomic DNA was sonicated to a range of 150-500bp and purified. For the M.SssI controls, genomic DNA was treated with M.SssI before sonication. DNA was adapter-ligated using the standard Illumina DNA sequencing protocol. 4μg of adapter-ligated DNA (or less, in a proportionately scaled-down reaction) was incubated overnight with 5mC antibody, after which the mix was incubated with beads, washed, eluted and purified using QIAquick MinElute spin columns. Purified DNA was PCR amplified for 18 cycles, size-selected to isolate fragments 150-200bp in length (not including the Illumina adapters) and sequenced on the Illumina Genome Analyzer IIx.     ChIP-seq: 10^7 cells were crosslinked with 1% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M glycine. Cross-linked cells were washed and lysed to obtain chromatin, which was sonicated to achieve a size-range of 200-500bps. 18ug sonicated chromatin was pre-cleared using protein-A-agarose beads supplemented with salmon sperm and incubated overnight at 4°C with 4.5 ug antibody. The following day the samples were incubated with protein-A-agarose beads supplemented with salmon sperm, washed, decrosslinked, eluted, and purified using QIAquick MinElute spin columns. Library preparation was performed according to the manufacturer's instructions and size-selected molecules (150-200bp in length, excluding adapters) were sequenced on the Illumina Genome Analyzer IIx.

tag: cell type

value: hTERT-immortalized WI-38 primary human lung fibroblasts

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #

tag: passage


title: Rrp41 rep1

description: 5' barcode: CACAGC

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0)

value: Rrp41-HTP (genomic)


title: ChIP seq CTCF A95

value: CTCF

value: Millipore


title: Rrp41 rep2

description: 5' barcode: GA


title: ChIP seq CTCF A39


title: ChIP seq Input A39


title: ChIP seq H3K27me3 A67


title: ChIP seq H3K27me3 B96


title: ChIP seq H3K27me3 A95


title: ChIP seq H3K27me3 A50


title: ChIP seq H3K27me3 A39


title: ChIP seq H3K27me3 19

value: WI-38 primary human lung fibroblasts


title: ChIP seq H3K27me3 A58


title: WC2_HSP3_WC2_42C

city: Utrecht

last: Wösten

address: Padualaan 8

country: Netherlands

institute: Utrecht University

data_processing: The sequenced reads were mapped to the genome sequence using the program Tophat 1.0.13 and Bowtie 0.12.5, using default settings with the exception of the minimum and maximum intron length (10 and 400 bp, respectively).

organism: Schizophyllum commune

source_name: Whole colony

growth_protocol: Colonies were grown from plug inoculum. Plugs of the compatible monokaryons were placed next to each other. Cultures were incubated for 6 days at 25 degrees C in continuous light. After this period, samples indicated with "42C" were placed at 42C for 1 hour. After that, they were placed back at 25C for 5 hours. Then RNA was isolated from each of the colonies.

extract_protocol: Three biological replicates were pooled. Colonies were frozen in liquid nitrogen and powdered. Total RNA was isolated using the Trizol reagent. The quality of the RNA was analysed on a RNA 6000 Lab-on-a-Chip using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The Illumina mRNA-Seq Sample Prep Kit was used to process the samples. The sample preparation was performed according the Illumina protocol "Preparing Samples for Sequencing of mRNA" (1004898 Rev. D).

tag: parental strain

value: Cross of H4-8 and H4-8b

tag: deleted gene

value: WC2 complemented with hsp3(promoter)-wc2


title: WC2_HSP3_WC2_25C


title: MeDIP seq B96

value: Diagenode


title: ChIP seq Input A95


title: MeDIP seq A95


title: MeDIP seq A67


title: WC2_25C


title: WC2_42C


title: MeDIP seq A50


title: MeDIP seq 19


title: WT_25C

value: wild-type


title: MeDIP seq A58


title: MeDIP seq A39


title: ChIP seq H3K4me3 19


title: E14 day6 ncRNA-seq

status: Public on Sep 22 2012

city: La Jolla

first: Pengfei

last: Yu

address: 9500 Gilman Drive MC 0419

department: Bioengineering

institute: University of California San Diego

data_processing:
The libraries for ncRNA and 5-hmC were sequenced on a HiSeq2000 using a TruSeq SBS sequencing kit version 2 and analyzed with pipeline version 1.8. The libraries of MeDIP-seq and MRE-seq were sequenced on Illumina GAII.
For small ncRNA sequencing data, The 3’ adapters were first trimmed from all 40bp short sequencing reads and short reads (<18bp) were removed after trimming. After that, reads were mapped into mouse mm9 genome using bowtie software with no mismatch in the first 18 seed sequences, and with no more than 5 alignments in the genome. Only the best alignments for each mappable reads were reported.
MRE-seq data were generated by index-sequencing(each index has 7bp), and total length of each sequenced read is 49bp. so the valid length of each read is 42bp. After trimming the indexes, the 42bp reads were mapped to mm9 genome by MAQ with an additional constraint that the 5′ end of a read must map to the CpG site within a MRE site
MeDIP-seq data were mapped to mm9 genome by MAQ
Sequence reads for 5hmC were mapped to mm9 using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome_build: mm9
Supplementary_files_format_and_content: BED

source_name: mouse embryonic stem cells (E14)

growth_protocol: E14(mESC) were plated onto gelatin-coated dishes in Dulbecco's modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM -mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Millipore ESG1107) in incubator set at 37 ºC in 5% CO2.

extract_protocol: MRE-seq was performed as described (NATURE| Vol 466|8 July 2010). Four parallel digests were performed (HpaII, Hin6I and SsiI are from Fermentas; HpyCH4IV is from NEB), each with 1 ug of DNA. Five units of enzyme per microgram DNA were added and incubated at 37˚C for 3 hrs. A second dose of five units-enzyme was added and the DNA was incubated for an additional 3 hrs. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose gel. A 100-500 bp gel slice was excised and gel-purified using Qiagen Qiaquick columns, eluting in 30 ul of Qiagen EB buffer. Library construction was performed using the Illumina Genomic DNA Sample kit with paired-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the klenow DNA polymerase was diluted 1:5 in water and 1 ul used per reaction. For paired-end oligo adapter ligation, adapters were diluted 1:10 in water and 1 ul used per reaction. After the second size selection, DNA was eluted in 36 ul EB buffer using Qiagen Qiaquick columns, and 12 ul used as template for PCR, using Illumina reagents and cycling conditions with 15 cycles. After cleanup with Qiagen MinElute columns, each library is examined by Quant-iT™ dsDNA HS Assay Kit (Qubit, Invitrogen, USA) and Agilent DNA Biaanalyzer (Agilent, USA). MeDIP-seq was performed as described (NATURE| Vol 466|8 July 2010). 3 ug DNA isolated as described above was sonicated to ,100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to paired-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 1 ug of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg/ml, Eurogentec). For this, DNA was heat-denatured at 95 ˚C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 ul primary antibody per microgram of DNA overnight at 4 ˚C with rocking agitation in 500 ml immunoprecipitation buffer (10mMsodium phosphate buffer, pH 7.0, 140mMNaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 2ul of rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson Immunoresearch) and 100 ml Protein A/G beads (Pierce Biotechnology) were added and incubated for an additional 2 h at 4 ˚C with agitation. After immunoprecipitation a total of six to ten immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific mouse IgG immunoprecipitation (Jackson Immunoresearch) was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/ml proteinase K for 2 h at 55 ˚C and then allowed to cool to room temperature. MeDIP and supernatant DNA were purified using Qiagen Qiaquic columns and eluted in 30 ul EB (Qiagen). Twelve cycles of PCR were performed on 10 ul of the immunoprecipitated DNA using the paired-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (192–592 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis. An aliquot of each library was diluted in EB to 5 ng/ul and 1 ul used as template in four independent PCR reactions to confirm enrichment for methylated and de-enrichment for unmethylated sequences, compared to 5 ng of input (sonicated DNA). Two positive controls (SNRPN and MAGEA1 promoters) and two negative controls (a CpG-less sequence on chromosome 15 and GAPDH promoter) were amplified (Supplementary). Cycling was 95 ˚C for 30 s, 58 ˚C for 30 s, 72 ˚C for 30 s with 30 cycles. PCR products were visualized by 1.5% agarose gel electrophoresis. DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Biotechnol. 2011, 29, 68-72). For ncRNA-seq, Total RNA was purified by Trizol Reagent (Invitrogen) and used as input to generate microRNA library by True-seq small RNA kit (Illumina). The RNA 3’ adapter is specifically modified to target microRNAs and other small RNAs that have a 3’ hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. The bands of library products from 145-160bp were cut and amplified for sequencing. The libraries were then quantitated by qPCR.

treatment_protocol: Guided differentiation procedures were preformed as following: 2×105 cells were seeded on the Collagen IV coated 10cm dishes (BD, 08-774-33) in serum free medium ESF-B (Itochu Corporation) supplemented with 0.1%BSA, 50M 2-Me and 10 ng/ml Activin A. Mediums were changed every day. Genomic DNAs and total RNAs were collected in day0, 4, and 6.

tag: development stage

value: Day 6

value: mouse embryonic stem cells (E14)

value: activin


title: E14 day6 MeDIP-seq

value: anti-methylcytidine

value: Eurogentec

tag: genetic background


title: E14 day4 MRE-seq

value: Day 4

tag: treatment


title: E14 day0 ncRNA-seq

value: Day 0


title: E14 day6 MRE-seq


title: E14 day4 ncRNA-seq


title: E14 day0 5-hmC ChIP-seq


title: MeDIP seq mSssI

value: hTERT-immortalized WI-38 primary human lung fibroblasts


title: E14 day4 MeDIP-seq