title: HudsonAlpha_ChipSeq_H1-hESC_USF-1_PCR1x

value: Rabbit polyclonal, USF-1 (C-20). Antibody Target:USF1

value: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.

tag: antibody vendorid

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

tag: softwareversion

value: Rabbit polyclonal, USF-1 (C-20).


title: HudsonAlpha_ChipSeq_ECC-1_ERalpha_a_Estradiol_10nM_v041610.2

status: Public on Sep 29 2011

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: 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

tag: cell lineage

value: endoderm

tag: antibody antibodydescription

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

tag: antibody targetdescription

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)

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: treatment description

value: 1 h with 10 nM Estradiol (Myers)

tag: controlid

tag: labexpid

tag: replicate

value: MACS

value: Santa Cruz Biotech

tag: treatment

value: 1 h with 10 nM Estradiol  (Myers)

tag: protocol

tag: protocol description

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

tag: replicate description

value: tier 1


title: HudsonAlpha_ChipSeq_SK-N-MC_RevXlinkChromatin_v041610.1

source_name: SK-N-MC

tag: cell

value: SK-N-MC

tag: cell organism

value: human

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: cell karyotype

value: cancer

value: ectoderm

tag: cell sex

value: F

tag: antibody

value: RevXlinkChromatin

value: No special treatment or protocol applies

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


title: HudsonAlpha_ChipSeq_GM12878_MEF2C_(SC-13268)_v041610.1

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell description

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

value: Goat polyclonal IgG, epitope mapping near the C-terminus of MEF2C of human origin. Antibody Target:MEF2C

value: This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq)

tag: antibody vendorid

tag: softwareversion


title: HudsonAlpha_ChipSeq_HepG2_ZBTB33_v041610.1

value: hepatocellular carcinoma

tag: antibody antibodydescription

value: Kaiso (6F8) Mouse monoclonal IgG1. Raised against amino acids 1-504 representing full length Kaiso of human origin. Recommended for detection of Kaiso of m, r, h, canine and chicken origin by WB, IP, IF and ELISA. Antibody Target:ZBTB33

tag: antibody targetdescription

value: KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: controlid

value: MACS

value: Santa Cruz Biotech

tag: treatment description


title: HudsonAlpha_ChipSeq_H1-hESC_CTCF_(SC-5916)_v041610.2

growth_protocol: missing

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)

tag: labexpid

tag: replicate

tag: treatment

tag: protocol

tag: protocol description

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

value: tier 1


title: HudsonAlpha_ChipSeq_A549_RevXlinkChromatin_DEX_100nM_PCR1x

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: 1 h with 100 nM Dexamethasone (Myers)

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

value: RevXlinkChromatin

value: 1 h with 100 nM DEX (Myers)

value: 1-cycle of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_A549_RevXlinkChromatin_EtOH_0.02pct_PCR1x

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell description

value: 1 h with 0.02% Ethanol (Myers)

tag: antibody

value: 1 h with 0.02% EtOH (Myers)


title: HudsonAlpha_ChipSeq_GM12878_Rad21_v041610.1

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

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:RAD21

tag: antibody targetdescription

value: Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14

value: abcam

tag: antibody vendorid

tag: softwareversion

value: MACS

value: Rabbit polyclonal

value: Abcam

value: No special treatment or protocol applies

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


title: HudsonAlpha_ChipSeq_ECC-1_ERalpha_a_DMSO_0.02pct_v041610.2

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: 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)

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: treatment description

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

tag: controlid

tag: labexpid

value: Santa Cruz Biotech

value: 1 h with 0.02% DMSO (Myers)

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

value: tier 1


title: HudsonAlpha_ChipSeq_K562_Pol2_v041610.1

value: ChipSeq

value: Chromatin IP Sequencing

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: replicate

value: mouse monoclonal, clone 8WG16

tag: treatment

tag: protocol

tag: protocol description


title: HudsonAlpha_ChipSeq_K562_Egr-1_v041610.1

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.

value: MACS

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

value: No special treatment or protocol applies

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

tag: replicate description


title: HudsonAlpha_ChipSeq_GM12878_ZEB1_(SC-25388)_v041610.2

tag: datatype

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

value: Rabbit polyclonal IgG, epitope corresponding to amino acids 39-140 mapping near the N-terminus of ZEB1 of human origin. Antibody Target:ZEB1

value: This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq).

value: Santa Cruz Biotechnology


title: HudsonAlpha_ChipSeq_K562_THAP1_(SC-98174)_v041610.1

tag: datatype description

value: Goat polyclonal IgG, epitope mapping near the C-terminus of THAP1 of human origin. Antibody Target:THAP1

value: The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq)

value: Santa Cruz Biotech

value: tier 1


title: HudsonAlpha_ChipSeq_GM12878_RevXlinkChromatin_v041610.2

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

tag: cell organism

value: human

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

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: RevXlinkChromatin

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


title: HudsonAlpha_ChipSeq_HepG2_ELF1_(SC-631)_v041610.1

value: hepatocellular carcinoma

tag: antibody antibodydescription

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

tag: antibody targetdescription

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)

tag: antibody vendorid

tag: softwareversion

value: MACS

value: No special treatment or protocol applies

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


title: HudsonAlpha_ChipSeq_K562_TAF7_(SC-101167)_v041610.1

value: Mouse monoclonal IgG, raised against recombinant TAF II p55 (TAF7) of human origin. Antibody Target:TAF7

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 (RefSeq).

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: controlid

tag: labexpid

tag: antibody

value: Santa Cruz Biotech

tag: treatment description


title: HudsonAlpha_ChipSeq_H1-hESC_SRF_PCR1x

value: ChipSeq

value: Chromatin IP Sequencing

value: Rabbit polyclonal. Antibody Target:SRF

value: Serum response transcription factor

tag: protocol description

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

tag: replicate

value: Rabbit polyclonal

tag: treatment

tag: protocol

value: 1-cycle of PCR (Myers)

tag: replicate description

value: tier 1


title: HudsonAlpha_ChipSeq_K562_SP2_(SC-643)_v041610.2

tag: datatype

tag: datatype description

value: Rabbit polyclonal IgG, epitope mapping near the N-terminus of SP2 of human origin. Antibody Target:SP2

value: This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq)

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


title: HudsonAlpha_ChipSeq_GM12891_Pol2-4H8_PCR1x

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

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

tag: labversion

value: MACS

value: Abcam

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_H1-hESC_SIX5_PCR1x

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Six5 (K-20) Goat polyclonal IgG, 200?g/ml. Epitope mapping near the C-terminus of Six5 of human origin. Recommended for detection of Six5 of human origin by WB, IF and ELISA. Antibody Target:SIX5

tag: antibody targetdescription

value: The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2.

value: Santa Cruz Biotechnology

value: Santa Cruz Biotech


title: HudsonAlpha_ChipSeq_GM12878_YY1_(SC-281)_PCR1x

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

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of YY1 of human origin. Antibody Target:YY1

value: YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1

tag: antibody vendorid

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

tag: softwareversion

value: 1-cycle of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_HepG2_FOXA2_(SC-6554)_v041610.1

value: hepatocellular carcinoma

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

tag: controlid

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


title: HudsonAlpha_ChipSeq_GM12891_Pol2_PCR1x

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: labexpid

value: MACS

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_GM12891_PU.1_PCR1x

value: ChipSeq

value: Chromatin IP Sequencing

value: Rabbit Polyclonal IgG. Antibody Target:PU1

value: Santa Cruz Biotechnology

value: Santa Cruz Biotech

tag: treatment description


title: HudsonAlpha_ChipSeq_H1-hESC_BCL11A_PCR1x

value: Mouse monoclonal [18B12DE6] to Ctip1. Raised against a cocktail of BCL11A fusion proteins. Reacts with human and mouse. Tested for ICC/IF, IHC-P, IP, WB. Antibody Target:BCL11A

value: This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity)

value: abcam

tag: protocol description

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

tag: cell sex

value: M

tag: antibody

value: Abcam

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_A549_GR_EtOH_0.02pct_PCR1x

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: Rabbit Polyclonal. Antibody Target:GR

value: Glucocorticoid Receptor

value: 1 h with 0.02% Ethanol (Myers)

tag: replicate

tag: treatment

value: 1 h with 0.02% EtOH (Myers)

tag: protocol

value: tier 1


title: HudsonAlpha_ChipSeq_T-47D_FOXA1_(SC-6553)_DMSO_0.02pct_v041610.2

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

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

value: Goat polyclonal IgG, epitope mapping at the C-terminus of FOXA1 of human origin. Antibody Target:FOXA1

value: This gene encodes a member of the forehead 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 (RefSeq).

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

value: MACS

value: 1 h with 0.02% DMSO (Myers)

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

tag: replicate description


title: HudsonAlpha_ChipSeq_GM12878_PAX5-C20_PCR1x

tag: cell description

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

tag: antibody antibodydescription

value: Goat polyclonal IgG, 200 micrograms/ml. Epitope mapping at the C-terminus of Pax-5 of human origin. Recommended for detection of Pax-5 of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:PAX5

value: This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation.

value: Santa Cruz Biotechnology

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

tag: labversion

value: Santa Cruz Biotech

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_GM12878_IRF4_(SC-6059)_PCR1x

value: Goat polyclonal IgG, epitope mapping at the C-terminus of IRF-4 of mouse origin. Antibody Target:IRF4

tag: antibody targetdescription

value: The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq).

tag: antibody vendorid

tag: softwareversion

value: 1-cycle of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_PANC-1_RevXlinkChromatin_PCR2x

value: ChipSeq

value: Chromatin IP Sequencing

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

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

tag: controlid

tag: labexpid

tag: cell lineage

value: endoderm

value: M

value: RevXlinkChromatin

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12891_TAF1_PCR1x

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

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

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

tag: antibody vendorname

tag: protocol description

value: MACS

tag: treatment description


title: HudsonAlpha_ChipSeq_H1-hESC_FOSL1_(SC-183)_v041610.2

value: Rabbit polyclonal IgG, epitope mapping at the N-terminus of FOSL1 of human origin. Antibody Target:FOSL1

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. (provided by RefSeq)

value: Santa Cruz Biotechnology

tag: replicate

tag: antibody

value: Santa Cruz Biotech

tag: treatment

value: No special treatment or protocol applies

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


title: HudsonAlpha_ChipSeq_GM12878_ZBTB33_PCR1x

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

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

value: Kaiso (6F8) Mouse monoclonal IgG1. Raised against amino acids 1-504 representing full length Kaiso of human origin. Recommended for detection of Kaiso of m, r, h, canine and chicken origin by WB, IP, IF and ELISA. Antibody Target:ZBTB33

value: KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA

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

tag: protocol

value: 1-cycle of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_K562_ATF3_v041610.1

tag: antibody antibodydescription

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of ATF3 of human origin. Antibody Target:ATF3

value: Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription.

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

tag: replicate description


title: HudsonAlpha_ChipSeq_HepG2_YY1_(SC-281)_v041610.1

tag: cell description

value: hepatocellular carcinoma

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of YY1 of human origin. Antibody Target:YY1

tag: antibody targetdescription

value: YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1

value: MACS


title: HudsonAlpha_ChipSeq_U87_RevXlinkChromatin_PCR2x

tag: cell

tag: cell organism

value: human

tag: cell karyotype

value: cancer

value: ectoderm

tag: cell sex

value: M

value: RevXlinkChromatin

value: No special treatment or protocol applies

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


title: HudsonAlpha_ChipSeq_K562_HEY1_PCR1x

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

value: ChipSeq

value: ChIP-Seq

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 lineage

value: mesoderm

value: F

value: HRT1 (C-20) Goat polyclonal IgG, 200 ?g/ml. Epitope mapping near the C-terminus of HRT1 of human origin

value: This gene encodes a nuclear protein belonging to the hairy and enhancer of split-related (HESR) family of basic helix-loop-helix (bHLH)-type transcriptional repressors. Expression of this gene is induced by the Notch and c-Jun signal transduction pathways. Two similar and redundant genes in mouse are required for embryonic cardiovascular development, and are also implicated in neurogenesis and somitogenesis. Alternative splicing results in multiple transcript variants.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: controlid

tag: labexpid


title: HudsonAlpha_ChipSeq_K562_CTCFL_(SC-98982)_v041610.1

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal IgG, epitope corresponding to amino acids 91-210 mapping within an internal region of BORIS(CTCFL) of human origin. Antibody Target:CTCFL

value: CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq)

value: Santa Cruz Biotechnology

tag: replicate

tag: softwareversion

value: MACS

tag: antibody

tag: treatment

tag: treatment description

tag: protocol description

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

value: tier 1


title: HudsonAlpha_ChipSeq_GM12878_BCL11A_PCR1x

tag: cell description

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

tag: antibody antibodydescription

value: Mouse monoclonal [18B12DE6] to Ctip1. Raised against a cocktail of BCL11A fusion proteins. Reacts with human and mouse. Tested for ICC/IF, IHC-P, IP, WB. Antibody Target:BCL11A

tag: antibody targetdescription

value: This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity)

value: abcam

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

tag: labversion

value: Abcam

value: No special treatment or protocol applies

tag: protocol

value: 1-cycle of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_K562_PU.1_PCR1x

value: ChipSeq

value: Rabbit Polyclonal IgG. Antibody Target:PU1

tag: antibody vendorname

tag: antibody vendorid


title: HudsonAlpha_ChipSeq_HepG2_HNF4G_(SC-6558)_v041610.1

value: Chromatin IP Sequencing

value: hepatocellular carcinoma

value: Goat polyclonal IgG, epitope mapping at the C-terminus of HNF4G of human origin. Antibody Target:HNF4G

value: Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene

tag: controlid

tag: labexpid

value: Santa Cruz Biotech


title: HudsonAlpha_ChipSeq_K562_SIX5_v041610.1

tag: datatype

tag: datatype description

value: Six5 (K-20) Goat polyclonal IgG, 200?g/ml. Epitope mapping near the C-terminus of Six5 of human origin. Recommended for detection of Six5 of human origin by WB, IF and ELISA. Antibody Target:SIX5

value: The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2.

value: Santa Cruz Biotechnology

value: MACS

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


title: HudsonAlpha_ChipSeq_GM12891_POU2F2_PCR1x

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: Oct-2(C-20) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of Oct-2 of human origin. Recommended for detection of Oct-2 of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:POU2F2

value: Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter.

tag: replicate

tag: softwareversion

value: tier 1


title: HudsonAlpha_ChipSeq_PFSK-1_RevXlinkChromatin_PCR2x

value: neuroectodermal cell line derived from a cerebral brain tumor, (PMID:1316433)

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: M

tag: antibody

value: RevXlinkChromatin

tag: treatment

value: No special treatment or protocol applies

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_PFSK-1_NRSF_PCR2x

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

tag: antibody antibodydescription

value: Mouse monoclonal. Antibody Target:NRSF

tag: antibody targetdescription

value: Neuron-restrictive silencer transcription factor

value: Dr. David Anderson at Caltech

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

tag: protocol description

value: David Anderson, Caltech

tag: treatment description


title: HudsonAlpha_ChipSeq_GM12878_p300_PCR1x

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

value: Rabbit Polyclonal. Antibody Target:P300

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

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

tag: labversion

value: MACS

value: Santa Cruz Biotech

tag: protocol

value: 1-cycle of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_PANC-1_NRSF_PCR2x

tag: datatype

tag: datatype description

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

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

tag: controlid

tag: labexpid

tag: replicate

value: tier 1


title: HudsonAlpha_ChipSeq_T-47D_ERalpha_a_Genistein_100nM_v041610.2

value: ChipSeq

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

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: 1 h with 100 nM Genistein (Myers)

value: Genestein 100nM treatment

tag: softwareversion

value: 1 h with 100 nM Genistein   (Myers)

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


title: HudsonAlpha_ChipSeq_GM12878_EBF1_(SC-137065)_PCR1x

value: Chromatin IP Sequencing

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

value: Mouse monoclonal IgG, raised against a.a. 1-300 mapping at the N-terminus of EBF of human origin. Antibody Target:EBF1

value: Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity).

tag: treatment

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_A549_GR_DEX_100nM_PCR2x

tag: cell description

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: Rabbit Polyclonal. Antibody Target:GR

value: Glucocorticoid Receptor

value: Santa Cruz Biotechnology

value: 1 h with 100 nM Dexamethasone (Myers)

value: MACS

value: Santa Cruz Biotech

value: 1 h with 100 nM DEX (Myers)

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_U87_NRSF_PCR2x

value: ChipSeq

tag: antibody antibodydescription

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)

tag: cell sex

value: M

tag: antibody

value: NRSF

value: David Anderson, Caltech

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


title: HudsonAlpha_ChipSeq_K562_MEF2A_v041610.1

value: Chromatin IP Sequencing

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of MEF-2 of human origin. Antibody Target:MEF2A

tag: antibody targetdescription

value: The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes.

tag: treatment description

value: No special treatment or protocol applies

tag: protocol description

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

value: tier 1


title: HudsonAlpha_ChipSeq_GM12878_TCF12_PCR1x

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

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.

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

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

tag: labversion

value: MACS

value: Santa Cruz Biotech

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_SIX5_PCR1x

tag: datatype

value: ChipSeq

value: Six5 (K-20) Goat polyclonal IgG, 200?g/ml. Epitope mapping near the C-terminus of Six5 of human origin. Recommended for detection of Six5 of human origin by WB, IF and ELISA. Antibody Target:SIX5

value: The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2.

tag: protocol

tag: replicate description


title: HudsonAlpha_ChipSeq_H1-hESC_SP1_PCR1x

tag: datatype description

value: Chromatin IP Sequencing

value: Sp1(E-3) is a mouse monoclonal antibody raised against amino acids 121-345 mapping near the N-terminus of Sp1 ofhuman origin. Recommended for detection of Sp1 of m, r and h origin by WB, IP, IF and ELISA. Antibody Target:SP1

value: SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter.

tag: controlid

tag: labexpid


title: HudsonAlpha_ChipSeq_A549_GR_EtOH_0.02pct_PCR2x

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: Rabbit Polyclonal. Antibody Target:GR

value: Glucocorticoid Receptor

value: 1 h with 0.02% Ethanol (Myers)

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

tag: replicate

tag: treatment

value: 1 h with 0.02% EtOH (Myers)

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_Pol2_PCR2x

tag: cell description

value: hepatocellular carcinoma

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: softwareversion

value: No special treatment or protocol applies

value: tier 1


title: HudsonAlpha_ChipSeq_HepG2_TAF1_PCR2x

value: ChipSeq

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

tag: antibody targetdescription

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

value: Santa Cruz Biotechnology

value: MACS

value: Santa Cruz Biotech


title: HudsonAlpha_ChipSeq_H1-hESC_NRSF_v041610.2

value: Chromatin IP Sequencing

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)

tag: cell sex

value: M

tag: antibody

value: NRSF

value: Mouse monoclonal

value: David Anderson, Caltech

tag: treatment description

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


title: HudsonAlpha_ChipSeq_A549_Pol2_EtOH_0.02pct_PCR2x

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

value: 1 h with 0.02% Ethanol (Myers)

tag: protocol description

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

value: 1 h with 0.02% EtOH (Myers)

value: 2-cycles of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_H1-hESC_Pol2_v041610.2

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: mouse monoclonal, clone 8WG16

value: No special treatment or protocol applies

tag: protocol

tag: labversion


title: HudsonAlpha_ChipSeq_H1-hESC_RevXlinkChromatin_v041610.2

tag: datatype description

tag: controlid

tag: cell

tag: cell organism

value: human

value: embryonic stem cells

tag: cell karyotype

value: normal

tag: cell lineage

value: inner cell mass

value: M

value: RevXlinkChromatin

tag: replicate description


title: HudsonAlpha_ChipSeq_GM12878_PAX5-N19_PCR1x

tag: cell description

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

tag: antibody antibodydescription

value: Goat polyclonal IgG, 200 micrograms /ml. Epitope mapping at the N-terminus of Pax-5 of human origin. Recommended for detection of Pax-5 of human origin by WB, IP, IF and ELISA. Antibody Target:PAX5

tag: antibody targetdescription

value: This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation.

value: Santa Cruz Biotechnology

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

tag: labexpid

tag: replicate

tag: softwareversion

value: MACS

value: Santa Cruz Biotech

tag: treatment

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_A549_GR_DEX_5nM_PCR1x

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: Rabbit Polyclonal. Antibody Target:GR

value: Glucocorticoid Receptor

tag: antibody vendorname

tag: antibody vendorid

tag: treatment description

value: 1 h with 5 nM Dexamethasone (Myers)

tag: protocol description

value: 1 h with 5 nM DEX (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_GM12878_GABP_PCR2x

tag: datatype description

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

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

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

tag: controlid

tag: labversion

tag: labversion description

value: No special treatment or protocol applies

tag: protocol

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_A549_GR_DEX_50nM_PCR1x

tag: cell description

value: Santa Cruz Biotechnology

value: 1 h with 50 nM Dexamethasone (Myers)

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

value: 1 h with 50 nM DEX (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_A549_GR_DEX_500pM_PCR1x

value: ChipSeq

tag: antibody antibodydescription

tag: antibody targetdescription

value: 1 h with 500 pM Dexamethasone (Myers)

value: MACS

value: 1 h with 500 pM DEX (Myers)

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_A549_Pol2_DEX_100nM_PCR2x

value: Chromatin IP Sequencing

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: 1 h with 100 nM Dexamethasone (Myers)

tag: labexpid

tag: replicate

value: 1 h with 100 nM DEX (Myers)


title: HudsonAlpha_ChipSeq_GM12878_Pol2_PCR2x

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

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

tag: softwareversion

tag: treatment

value: No special treatment or protocol applies

value: 2-cycles of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_K562_RevXlinkChromatin_PCR1x

tag: datatype

value: ChipSeq

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: antibody

value: RevXlinkChromatin


title: HudsonAlpha_ChipSeq_GM12878_USF-1_PCR2x

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal, USF-1 (C-20). Antibody Target:USF1

value: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: protocol description

tag: controlid

value: MACS

tag: treatment description


title: HudsonAlpha_ChipSeq_GM12878_NRSF_PCR2x

tag: cell description

tag: antibody antibodydescription

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)

tag: labversion

tag: labversion description

tag: protocol

tag: replicate description


title: HudsonAlpha_ChipSeq_GM12878_SRF_PCR2x

tag: datatype

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

value: Rabbit polyclonal. Antibody Target:SRF

tag: antibody targetdescription

value: Serum response transcription factor

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

tag: labexpid

tag: replicate

tag: softwareversion

tag: treatment

value: No special treatment or protocol applies

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_SK-N-MC_FOXP2_PCR2x

value: ChipSeq

tag: datatype description

value: Rabbit polyclonal, raised against C-terminal 127 amino acids of FOXP2 of human origin. Antibody Target:FOXP2

value: This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech

tag: antibody vendorname

value: abcam

tag: antibody

value: rabbit polyclonal

value: transcriptional repressor, involved in development of speech

value: Abcam

value: tier 1


title: HudsonAlpha_ChipSeq_HCT-116_YY1_(SC-281)_v041610.1

value: Chromatin IP Sequencing

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of YY1 of human origin. Antibody Target:YY1

value: YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: controlid

value: MACS

value: Santa Cruz Biotech

tag: protocol description

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


title: HudsonAlpha_ChipSeq_GM12878_RevXlinkChromatin_PCR1x

tag: cell description

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

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

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: RevXlinkChromatin

tag: treatment description

value: No special treatment or protocol applies

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_NRSF_PCR2x

tag: datatype

value: ChipSeq

value: hepatocellular carcinoma

tag: antibody antibodydescription

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

value: David Anderson, Caltech

tag: protocol

value: 2-cycles of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_H1-hESC_HDAC2_(SC-6296)_v041610.2

value: Chromatin IP Sequencing

value: Goat polyclonal IgG, epitope mapping at the C-terminus of HDAC2 of human origin. Antibody Target:HDAC2

tag: antibody targetdescription

value: This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq)

value: Santa Cruz Biotechnology

tag: labexpid

tag: replicate

tag: softwareversion

value: MACS

value: Santa Cruz Biotech

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

value: tier 1


title: HudsonAlpha_ChipSeq_HepG2_GABP_PCR2x

value: ChipSeq

tag: datatype description

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

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

tag: antibody vendorname

tag: labversion

tag: treatment

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_T-47D_CTCF_(SC-5916)_DMSO_0.02pct_v041610.2

tag: cell description

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

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)

tag: antibody vendorid

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

tag: controlid

value: 1 h with 0.02% DMSO (Myers)

tag: protocol description


title: HudsonAlpha_ChipSeq_GM12878_BCL3_v041610.1

value: Chromatin IP Sequencing

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

value: Rabbit polyclonal. Bcl-3(C-14) is an affinity purified antibody raised against a peptide mapping at the C-terminus of Bcl-3 of human origin. Recommended for detection of Bcl-3 of mouse, rat and human origin by WB, IP, IF and ELISA. Antibody Target:BCL3

value: This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq).

value: Bcl-3(C-14) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of Bcl-3 of human origin. Recommended for detection of Bcl-3 of m, r and h origin by WB, IP, IF and ELISA.

tag: treatment description

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


title: HudsonAlpha_ChipSeq_GM12878_RXRA_PCR1x

tag: datatype

value: RXRa(D-20) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the N-terminus of RXRalpha of human origin. Recommended for detection of RXRalpha of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:RXRA

value: Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators.

value: Santa Cruz Biotechnology

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

value: Santa Cruz Biotech

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12878_RevXlinkChromatin_PCR2x

value: ChipSeq

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

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: antibody

value: RevXlinkChromatin

value: No special treatment or protocol applies

value: 2-cycles of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_H1-hESC_RevXlinkChromatin_PCR1x

value: Chromatin IP Sequencing

tag: labexpid

tag: cell organism

value: human

value: embryonic stem cells

value: inner cell mass

value: M

tag: protocol

tag: replicate description


title: HudsonAlpha_ChipSeq_GM12878_SP1_PCR1x

tag: datatype description

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

tag: antibody antibodydescription

value: Sp1(E-3) is a mouse monoclonal antibody raised against amino acids 121-345 mapping near the N-terminus of Sp1 ofhuman origin. Recommended for detection of Sp1 of m, r and h origin by WB, IP, IF and ELISA. Antibody Target:SP1

tag: antibody targetdescription

value: SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter.

tag: antibody vendorname

value: Santa Cruz Biotechnology

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

tag: replicate

tag: softwareversion

value: MACS


title: HudsonAlpha_ChipSeq_ECC-1_GR_DEX_100nM_v041610.2

value: ChipSeq

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

value: Rabbit Polyclonal. Antibody Target:GR

value: Glucocorticoid Receptor

tag: antibody vendorid

value: 1 h with 100 nM Dexamethasone (Myers)

tag: controlid

value: Santa Cruz Biotech

tag: treatment

value: 1 h with 100 nM DEX (Myers)

tag: protocol description

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


title: HudsonAlpha_ChipSeq_GM12878_SIX5_PCR1x

tag: datatype

value: Chromatin IP Sequencing

value: Six5 (K-20) Goat polyclonal IgG, 200?g/ml. Epitope mapping near the C-terminus of Six5 of human origin. Recommended for detection of Six5 of human origin by WB, IF and ELISA. Antibody Target:SIX5

value: The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2.

tag: treatment description

value: No special treatment or protocol applies

value: 1-cycle of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_GM12891_PAX5-C20_v041610.1

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: Goat polyclonal IgG, 200 micrograms/ml. Epitope mapping at the C-terminus of Pax-5 of human origin. Recommended for detection of Pax-5 of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:PAX5

value: This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation.

value: Santa Cruz Biotechnology

tag: labexpid

value: Goat polyclonal IgG, 200 ?g/ml. Epitope mapping at the C-terminus of Pax-5 of human origin. Recommended for detection of Pax-5 of m, r and h origin by WB, IP, IF, IHC(P) and ELISA

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


title: HudsonAlpha_ChipSeq_GM12892_PAX5-C20_v041610.1

value: ChipSeq

value: MACS


title: HudsonAlpha_ChipSeq_HepG2_TCF12_PCR1x

value: hepatocellular carcinoma

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.

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

value: Santa Cruz Biotech


title: HudsonAlpha_ChipSeq_SK-N-SH_RA_CTCF_v041610.2

value: Chromatin IP Sequencing

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

value: rabbit polyclonal

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


title: WT_NoPi_Nucleosome

status: Public on Sep 28 2011

city: Boston

first: Xu

last: Zhou

state: MA

address: 300 Longwood Ave

department: Pediatrics

institute: Boston Children's Hospital

data_processing:
Alignment: Sequence reads were obtained and mapped to the S. cerevisiae (2003) genomes using the Illumina Genome Analyzer Pipeline. All reads uniquely mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 80 bp to create summary windows.
Paired-end Data: the average insert size for WT_NoPi_Nucleosome is 154 bp, with standard deviation of 22.8 bp

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Phosphate-free synthetic complete medium was prepared from Difco phosphate-free Yeast Nitrogen Base and supplemented to final concentration of 2% glucose, 1.5 mg/ml potassium chloride, 0.1 mg/ml sodium chloride and amino acids, as described previously (Lam et al., 2008).  Monobasic potassium phosphate was added to phosphate-free medium to make high phosphate (Pi) medium containing a final concentration of 10 mM inorganic phosphate.  All media were adjusted to pH 4.0 with HCl (Thomas and O'Shea, 2005).  Yeast strains were grown at 30 °C with shaking and cell samples were collected at early/mid-logarithmic phase (OD600 0.3 ~ 0.4).

extract_protocol: ~100 OD units of cells were collected for high Pi and no Pi conditions.  Cells were crosslinked with 1% formaldehyde for 15 minutes and then quenched with 125 mM glycine for 5 minutes at room temperature.  Cells were collected by centrifugation, immediately washed with cold PBS buffer (137 mM NaCl, 2.7 mM KCl, 10 mM Sodium phosphate dibasic, 2 mM potassium phosphate monobasic, pH 7.4), and mechanically lysed with glass beads in lysis buffer (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate).  Chromatin was fragmented by sonication of the lysate and the supernatant was pre-cleared with protein G dynabeads (Invitrogen) for 2 hours at 4 °C.  M-280 dynabeads (Invitrogen) were blocked with lysis buffer containing 1% cold fish skin gelatin (Sigma-Aldrich) at 4 °C for 2 hours and then incubated with pre-cleared cell lysate overnight at 4°C.  After incubation, the dynabeads were washed with lysis buffer, high salt wash buffer (50 mM HEPES, pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate), lithium wash buffer (10 mM Tris/HCl, pH 8.0, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.1% Na-Deoxycholate), and SDS wash buffer (10 mM Tris/HCl, pH 8.0, 1 mM EDTA, 3% SDS) for 2 - 2 minutes at room temperature, and 1- 2 minutes with TE buffer (10 mM Tris/HCl, pH 8.0, 1 mM EDTA).  Crosslinks were reversed by incubation of samples at 65 °C for at least 6 hours in 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.8% SDS.  RNA and proteins in the samples were digested with 20 ug/ml RNase at 37 °C for 2 hours and 0.2 mg/ml proteinase K for 2 hours at 55 °C.  DNA was then purified with phenol-chloroform extraction and precipitated with ethanol.  5% of the volume of cell lysate was removed after sonication and used to prepare the input DNA for each ChIP experiment.  ChIP DNA concentration was estimated with the Pico-green DNA detection kit (Invitrogen).  Sequencing libraries were prepared following the Illumina protocol and libraries with size between 200 to 300 bp were selected for PCR amplification and assayed with an Agilent bioanalyzer.

treatment_protocol: To induce the Pi starvation response, yeast cells were first grown in 10 mM Pi medium to early/mid-logarithmic phase.  Cells were then harvested by filtering and washed 2 - 3 times with no Pi medium pre-warmed to 30 °C.  Finally, cells were resuspended in pre-warmed no Pi medium and grown at 30 °C for 1 hour.

tag: strain

tag: variant

value: wild type


title: Pho4_Input_NoPi


title: Pho2_Input_HighPi

value: pho2::N-Avitag-PHO2  ura3::pRS306-birA


title: Pho4_Input_HighPi


title: WT_ChIP_HighPi

description: replicate 1,2,3 and 4


title: Pho4_ChIP_dPHO80dCBF1

description: replicate 1 and 2

value: pho4::PHO4-C-Avitag-TRP1  cbf1::HIS3MX6  pho80::CgLEU2  ura3::pRS306-birA


title: Cbf1_ChIP_NoPi


title: Pho2_ChIP_HighPi


title: Cbf1_Input_NoPi


title: Pho4_ChIP_dPho2_NoPi

value: pho4::PHO4-C-Avitag- TRP1  pho2::HI3MX6  ura3::pRS306-birA


title: WT_Input_NoPi


title: Pho4_ChIP_dPHO80

value: pho4::PHO4-C-Avitag-TRP1  pho80::HIS3MX6  ura3::pRS306-birA


title: Cbf1_ChIP_HighPi

description: replicate 1 and 2


title: Pho2_ChIP_NoPi

description: replicate 1 and 2


title: Pho4_ChIP_NoPi

description: replicate 1 and 2


title: WT_ChIP_NoPi


title: Pho4_ChIP_HighPi


title: WT_Input_HighPi


title: Normal colonic mucosa adjacent to CIMP-H tumor

status: Public on Sep 27 2011

city: Los Angeles

first: Benjamin

last: Berman

department: USC Epigenome Center

institute: University of Southern California

description:
biospecimen repository sample id: 17808
SRA sample id: SRS255313

data_processing:
Genome build hg18 (NCBI v.36) was used for all analyses. MAQ was used for sequence alignment, using the Ã-cÃ option to match any C or T in the sequencing read to a C in the reference genome. SAMTOOLS37 was used to perform processing and merging of BAM files, and duplicate reads starting at the same genomic position were removed for each of the two sequencing libraries per sample. Reads were also filtered out if they had a MAQ mapping quality score of less than 30 - this removes alignments with many mismatches as well as those reads aligning equally well to multiple locations in the genome. An in-house Java library (http://ngsgenomelibs.svn.sourceforge.net/viewvc/ngsgenomelibs/trunk/src/edu/usc/epigenome/scripts/SamToMethyldbOffline.java) was used to transform BAM alignments to percent alignment for each cytosine in the genome. Each cytosine in the reference genome was included for analysis if it was covered by 3 or more C or T reads on the bisulfite converted strand, greater than 90% of all reads on this strand were either C or T, and greater than 90% of reads on the opposite strand (i.e. the ÃGÃ strand, not affected by bisulfite conversion) were G. Cytosines were considered high-confidence CpGs if greater than 90% of reads at the following position were G, and high-confidence CpHs if greater than 90% of reads at the next position were H (A,C,T). For the colon tumor sample, of 49,057,680 reference genome CpGs covered by sequence reads, 96.2% (47,179,160) were classified as high-confidence CpGs.
percentmeth: Wiggle file where each value is the percent of reads methylated at each CpG position in the genome (number of actual methylated reads is equal to readcounts value times percentmeth value)
readcounts: Wiggle file where each value is the number of reads at each CpG position in the genome

source_name: Normal colon mucosa

growth_protocol: Tumor and adjacent normal mucosa DNA were obtained from the Ontario Tumor Bank (accessions OTB14838T, tumor; OTB14838N, adjacent). Informed consent was obtained for all subjects and was approved for the described analyses by the University of Southern California Institutional Review Board.

extract_protocol: DNA libraries from each sample were prepared using a method similar to [Lister, 2009], but with a number of customizations. Briefly, sequencing adapters with fully methylated cytosines (Integrated DNA Technologies, Coralville, IA) were used to create Illumina GAIIx sequencing libraries, followed by bisulfite conversion (Zymo EZ DNA Methylation kit, Zymo Research, Orange, CA) and PCR amplification. Two libraries were made for each sample, and each library was PCR amplified by dividing into nine independent PCR reactions and pooling PCR products. Attachment of the library DNA to the Genome Analyzer flow cell was performed on an Illumina Cluster Station fluidics device. Single-end DNA sequencing (76 bp reads) was performed using the Illumina Genome Analyzer IIx as described in7. A total of 63 and 67 lanes were sequenced for the normal colon and tumor samples, respectively.

tag: tissue type

value: normal


title: HudsonAlpha_ChipSeq_SK-N-SH_NRSF_PCR2x

source_name: SK-N-SH

value: ChipSeq

tag: datatype description

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

value: MACS

value: David Anderson, Caltech

value: No special treatment or protocol applies

tag: protocol

value: 2-cycles of PCR (Myers)

tag: replicate description

value: tier 1


title: 4131 caries positive dizygotic twin pair of 4132

status: Public on Sep 26 2011

city: Rockville

first: Vasily

middle: A

last: Sharov

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: JCVI

description:
Metagenomic RNA from Dental Sample 4131
4131_CP_DZ_PairTo_4132

library_source: transcriptomic

data_processing: Raw sequence data generated by GA II were processed, filtered and normalized using the Illumina pipeline (www.illumina.com) to generate raw sequence reads files. All reads were then  aligned to the annotataed Streptococcus sanguinis SK36 protein coding sequences to calculate expression values for every gene in RPKM using CLC Bio Genomic Workbench with default parameters: minimum length fraction (0.9), minimum similarity fraction (0.8), maximum number of hits per read (10).

molecule: total RNA

organism: human oral metagenome

source_name: 3307 Dental Plaque

growth_protocol: N/A.  Samples were human dental plaque samples.

extract_protocol: Library construction was performed according to the Illumina protocol. (www.illumina.com)

treatment_protocol: Five micrograms of total RNA from each sample were enriched for microbial RNA using Ambion's MicrobEnrich kit.  Ten nanograms of the enriched RNA were then amplified using Nugen's OvationÂ® RNA-Seq kit.  Two micrograms of amplified, enriched cDNA were further enriched for messenger RNA through subtractive hybridization of ribosomal content.

tag: sample type

value: dental plaque

tag: patient id

tag: twin pair

tag: twin type

value: dizygotic twin

tag: disease state

value: caries positive


title: 3307 caries negative dizygotic twin pair of 3306

description:
Metagenomic RNA from Dental Sample 3307
3307_CN_DZ_PairTo_3306

source_name: 3306 Dental Plaque

value: caries negative


title: 3306 caries positive dizygotic twin pair of 3307

description:
Metagenomic RNA from Dental Sample 3306
3306_CP_DZ_PairTo_3307

source_name: 3215 Dental Plaque


title: Stage 3, CIMP-H colon tumor with G12D KRAS mutation

description:
biospecimen repository sample id: 14838
SRA sample id: SRS255405

source_name: CIMP-H colon tumor

value: adenocarcinoma


title: 4132 caries negative dizygotic twin pair of 4131

description:
Metagenomic RNA from Dental Sample 4132
4132_CN_DZ_PairTo_4131

source_name: 4131 Dental Plaque


title: Pho2_Input_NoPi

value: pho2::N-Avitag-PHO2  ura3::pRS306-birA


title: 2992 caries negative dizygotic twin pair of 2991

description:
Metagenomic RNA from Dental Sample 2992
2992_CN_DZ_PairTo_2991

source_name: 2991 Dental Plaque


title: SYTSSX2_FLAG_ChIP

city: Nashville

first: Josiane

last: Eid

address: 2220 Pierce Avenue

institute: Vanderbilt University

data_processing:
The Illumina Analysis Pipeline was used for image analysis and base calling to generate fastq sequence files.
Bowtie (Langmead B et al, 2009. Genome Biol 10:R25) was used to align the sequences to the mouse genome.  The files generated by Bowtie were used as input for Model-based Analysis of ChIPSeq (MACS) (Zhang Y et al, 2008. Genome Biol 9:R137) which was used to identify peaks.

organism: Mus musculus

growth_protocol: Cells were maintained in DMEM containing 10% FBS, 1% penicillin/streptomycin at 37˚C, 5% CO2.

extract_protocol: ChIP was performed according to previously described methods (Boyer LA et al, 2005. Cell 122:947-56) with some modifications using either control IgG (Abcam) or anti-FLAG (Sigma) antibodies.  The purified ChIP DNA was further sonicated prior to end repair, addition of 'A' base to DNA fragment 3' ends, and ligation of adaptors using Illumina ChIPSeq DNA sample prep kit.  Ligated DNA  samples were gel purified and amplified by PCR.  PCR products were purified and diluted to 10nM for cluster generation.

treatment_protocol: Cells were infected with retrovirus carrying SYTSSX2 expression vector for 6h, then medium was changed to fresh growth medium.  Cells were allowed to grow for 48 hours post-infection before chromatin immunoprecipitation.

tag: cell type

value: SYTSSX2-expressing C2C12 myoblasts

tag: chip antibody

value: anti-FLAG antibody (Sigma)


title: 2991 caries positive dizygotic twin pair of 2992

description:
Metagenomic RNA from Dental Sample 2991
2991_CP_DZ_PairTo_2992

source_name: 2931 Dental Plaque


title: 2930 caries negative dizygotic twin pair of 2931

description:
Metagenomic RNA from Dental Sample 2930
2930_CN_DZ_PairTo_2931

source_name: 2355 Dental Plaque


title: 2931 caries positive dizygotic twin pair of 2930

description:
Metagenomic RNA from Dental Sample 2931
2931_CP_DZ_PairTo_2930

source_name: 2930 Dental Plaque


title: 2354 caries positive dizygotic twin pair of 2355

description:
Metagenomic RNA from Dental Sample 2354
2354_CP_DZ_PairTo_2355

source_name: 2284 Dental Plaque


title: 2355 caries positive dizygotic twin pair of 2354

description:
Metagenomic RNA from Dental Sample 2355
2355_CP_DZ_PairTo_2354

source_name: 2354 Dental Plaque


title: 2283 caries positive dizygotic twin pair of 2284

description:
Metagenomic RNA from Dental Sample 2283
2283_CP_DZ_PairTo_2284

source_name: 2270 Dental Plaque


title: 2270 caries negative dizygotic twin pair of 2269

description:
Metagenomic RNA from Dental Sample 2270
2270_CN_DZ_PairTo_2269

source_name: 2269 Dental Plaque


title: 2269 caries positive dizygotic twin pair of 2270

description:
Metagenomic RNA from Dental Sample 2269
2269_CP_DZ_PairTo_2270

source_name: 2242 Dental Plaque


title: 2234 caries negative dizygotic twin pair of 2233

description:
Metagenomic RNA from Dental Sample 2234
2234_CN_DZ_PairTo_2233

source_name: 2233 Dental Plaque


title: 2233 caries negative dizygotic twin pair of 2234

description:
Metagenomic RNA from Dental Sample 2233
2233_CN_DZ_PairTo_2234

source_name: 2225 Dental Plaque


title: 2226 caries positive monozygotic twin pair of 2225

description:
Metagenomic RNA from Dental Sample 2226
2226_CP_MZ_PairTo_2225

source_name: 2192 Dental Plaque

value: monozygotic twin


title: 2191 caries negative monozygotic twin pair of 2192

description:
Metagenomic RNA from Dental Sample 2191
2191_CN_MZ_PairTo_2192

source_name: 2170 Dental Plaque


title: 2192 caries negative monozygotic twin pair of 2191

description:
Metagenomic RNA from Dental Sample 2192
2192_CN_MZ_PairTo_2191

source_name: 2191 Dental Plaque


title: 3215 caries negative monozygotic twin pair of 3214

description:
Metagenomic RNA from Dental Sample 3215
3215_CN_MZ_PairTo_3214

source_name: 3214 Dental Plaque


title: 2170 caries positive monozygotic twin pair of 2169

description:
Metagenomic RNA from Dental Sample 2170
2170_CP_MZ_PairTo_2169

source_name: 2169 Dental Plaque


title: 2062 caries negative dizygotic twin pair of 2061

description:
Metagenomic RNA from Dental Sample 2062
2062_CN_DZ_PairTo_2061

source_name: 2061 Dental Plaque


title: 2011 caries positive dizygotic twin pair of 2012

description:
Metagenomic RNA from Dental Sample 2011
2011_CP_DZ_PairTo_2012

source_name: 2955 Dental Plaque


title: 3214 caries positive monozygotic twin pair of 3215

description:
Metagenomic RNA from Dental Sample 3214
3214_CP_MZ_PairTo_3215

source_name: 2992 Dental Plaque


title: 2061 caries positive dizygotic twin pair of 2062

description:
Metagenomic RNA from Dental Sample 2061
2061_CP_DZ_PairTo_2062

source_name: 2012 Dental Plaque


title: 2012 caries positive dizygotic twin pair of 2011

description:
Metagenomic RNA from Dental Sample 2012
2012_CP_DZ_PairTo_2011

source_name: 2011 Dental Plaque


title: 2169 caries negative monozygotic twin pair of 2170

description:
Metagenomic RNA from Dental Sample 2169
2169_CN_MZ_PairTo_2170

source_name: 2062 Dental Plaque


title: 2954 caries positive dizygotic twin pair of 2955

description:
Metagenomic RNA from Dental Sample 2954
2954_CP_DZ_PairTo_2955

source_name: 2310 Dental Plaque


title: 2955 caries positive dizygotic twin pair of 2954

description:
Metagenomic RNA from Dental Sample 2955
2955_CP_DZ_PairTo_2954

source_name: 2954 Dental Plaque


title: 2310 caries negative dizygotic twin pair of 2309

description:
Metagenomic RNA from Dental Sample 2310
2310_CN_DZ_PairTo_2309

source_name: 2309 Dental Plaque


title: 2284 caries positive dizygotic twin pair of 2283

description:
Metagenomic RNA from Dental Sample 2284
2284_CP_DZ_PairTo_2283

source_name: 2283 Dental Plaque


title: 2309 caries negative dizygotic twin pair of 2310

description:
Metagenomic RNA from Dental Sample 2309
2309_CN_DZ_PairTo_2310

source_name: 2126 Dental Plaque


title: 2126 caries positive monozygotic twin pair of 2125

description:
Metagenomic RNA from Dental Sample 2126
2126_CP_MZ_PairTo_2125

source_name: 2125 Dental Plaque


title: Control_IgG_ChIP

value: IgG antibody (Abcam)


title: 2241 caries positive dizygotic twin pair of 2242

description:
Metagenomic RNA from Dental Sample 2241
2241_CP_DZ_PairTo_2242

source_name: 2234 Dental Plaque


title: 2242 caries positive dizygotic twin pair of 2241

description:
Metagenomic RNA from Dental Sample 2242
2242_CP_DZ_PairTo_2241

source_name: 2241 Dental Plaque


title: 2225 caries negative monozygotic twin pair of 2226

description:
Metagenomic RNA from Dental Sample 2225
2225_CN_MZ_PairTo_2226

source_name: 2226 Dental Plaque


title: 2051 caries negative monozygotic twin pair of 2052

description:
Metagenomic RNA from Dental Sample 2051
2051_CN_MZ_PairTo_2052

source_name: 2051 Dental Plaque


title: 2052 caries negative monozygotic twin pair of 2051

description:
Metagenomic RNA from Dental Sample 2052
2052_CN_MZ_PairTo_2051

source_name: 2052 Dental Plaque


title: 2125 caries positive monozygotic twin pair of 2126

description:
Metagenomic RNA from Dental Sample 2125
2125_CP_MZ_PairTo_2126


title: 3' RNA-seq Watson strand Yra1-depleted cells_and_3' RNA-seq Crick strand Yra1-depleted cells

status: Public on Sep 25 2011

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description: oligo-dT primed cDNA

data_processing: Single-end 25 base reads (after removing oligodT(12) and barcodes) were mapped to the UCSC yeast genome (sacCer2, SGD genome Jun 2008 assembly) with Bowtie version 0.12.5. We generated bedGraph profiles representing the number of aligned reads at each genomic position (bp). The mapping process was performed in two steps to eliminate artifacts due to internal priming at runs of A's. First, we aligned the reads after removing the seven nucleotides only at the 5? end (three nucleotide barcode and the four oligo dT). These mapped reads were discarded as artefacts due to internal priming at runs of As. In the second step, we realigned the reads unmapped in the first step after removing the 15 nucleotides at the 5? end comprising the barcode and T12).

molecule: polyA RNA

source_name: yeast poly A+ mRNA

growth_protocol: cells were grown in SC 2%raffinose+galactose to O.D. ~ 0.2 at 25Âº then shifted to SC 2% glucose for 8 hr

extract_protocol:
3' end cDNA library construction
Oligo-dT primed libraries of 3' ends were made as described (Mangone, M. et al. Science 329, 432-435, 2010) with modifications outlinedbelow and sequenced with the Illumina Genome Analyzer IIx. Single-end 25 base reads (after removing oligodT(12) and barcodes) were mapped to the UCSC yeast genome (sacCer2, SGD genome Jun 2008 assembly) with Bowtie version 0.12.5.
First-strand cDNA synthesis (20µl final volume) was with SuperScript II RT (Invitrogen) at 42º according to the manufacturer's instructions. Poly(A)+ RNA (200-400ng) purified from WT (W3031B) or Yra1-depleted (DBY1276-2) cells using BioMag Oligo (dT)20 particles (Polysciences, Inc.) was primed with the following biotinylated oligo at 0.5mg/ml:
5'-biotin-ACACTCTTTCCCTACACGACGCTCTTCCGATCTXXTTTTTTTTTTTTVN-3' where XX represents a barcode (CG or GC). The second strand (100µl final volume) was synthesized using DNA polymerase I (30U, Fermentas) in the presence of RNaseH (1U, Fisher Scientific) at 15 'C for 2.5 hours and purified using a QIAquick column (Qiagen). cDNA was digested with NlaIII, purified on a QIAquick column and immobilized on 25µl of Streptavidin Dynabeads M-280 (Invitrogen) in B&W buffer (5mM Tris, pH7.5, 0.5mM EDTA, 1M NaCl). Streptavidin-bound cDNA was washed twice with B&W buffer and twice with of 10mM Tris, pH 8 (500µl each wash), and ligated to 5µl (50 pmols) annealed NlaIII-linkers (top: 5'-5phos-CATGGGAAGAGCGGTTCAGCAGGAATGCCGAG-3'; bottom: 5'-CTCGGCATTCCTGCTGAACCGCTCTTCC-3') using T4 DNA ligase (5U, Fermentas) overnight at 16'C (30µl final volume). The beads were washed at room temperature twice with B&W buffer and twice with TE (500µl each wash). Beads were resuspended in 200µl TE and cDNA was eluted by incubation with 200µl phenol/chloroform for 30 minutes at 65'C with frequent vortexing. 3'-cDNA libraries were purified using a QIAquick column and PCR-amplified (18 cycles) using Phusion polymerase (NEB) using Illumina paired end primers.

tag: genotype/variation

value: DBY1272-2 (GAL1-YRA1 W303 background)

tag: growth conditions

value: cells were grown in SC 2%raffinose+galactose to O.D. ~ 0.2 at 25º then shifted to SC 2% glucose for 8 hr


title: wild-type replicate 2

status: Public on Sep 24 2011

city: Fort Collins

first: Mark

last: Rogers

address: 1873 Campus Delivery

department: Computer Science

institute: Colorado State University

description: 76nt reads

data_processing: TopHat 1.0.14/BowTie 0.12.5;command: tophat -a 10 -g 1 -F 0 -p 6 --segment-length=26 --segment-mismatches=2 -i 40 -I 5000 --min-coverage-intron=40 --max-coverage-intron=5000 --min-segment-intr on=40 --max-segment-intron=5000 a_thaliana arabidopsis_seedling_wt_a.fq,arabidopsis_seedling_wt_b.fq

organism: Arabidopsis thaliana

source_name: two-week-old seedling

growth_protocol: Total RNA from 2-week-old Arabidopsis thaliana (ecotype Columbia) seedlings grown on MS plates and isolated using RNeasy Plant Mini Kit from Qiagen.

extract_protocol: Isolation of poly (A) mRNA and preparation of cDNA library were carried out using the Illumina TrueSeq RNA kit

treatment_protocol: To remove any contaminating DNA, RNA was treated with DNAse.

tag: ecotype

value: Columbia

tag: developmental stage

value: 2-week-old seedling


title: wild-type replicate 1

description: 76nt reads


title: Yale_ChipSeq_CH12_H3K4me3_IgG-Yale

status: Public on Sep 20 2011

tag: lab

value: Yale-m

tag: lab description

value: Weissman - Yale University

tag: datatype

value: ChipSeq

value: ChIP-Seq

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-Yale

tag: control description

value: Input signal from Mouse IgG ChIP-seq prepared at Yale

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: replicate

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: 3' RNA-seq Watson strand WT cells_and_3' RNA-seq Crick strand WT cells

description: oligo-dT primed cDNA

tag: genotype/variation

tag: growth conditions

value: cells were grown in SC 2%raffinose+galactose to O.D. ~ 0.2 at 25º then shifted to SC 2% glucose for 8 hr


title: Yale_ChipSeq_CH12_Input_IgG-Yale

tag: lab

value: Yale-m

tag: lab description

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: replicate description

value: tier 1


title: Testis_30 days

status: Public on Sep 23 2011

city: haerbin

first: Chuanjiang

last: Lian

address: maduan Street 427

country: China

institute: HVRI,CAAS

description: Junmu-1 boars (a white, Chinese indigenous breed).

data_processing:
Alignment: Raw sequence reads were processed into clean full-length reads using the BGI small RNA pipeline. First, all low-quality reads were removed from the raw sequence, and the 3' adapter reads, 5' adapter contaminants, sequences containing the polyA tail and those smaller than 18 nt were also discarded. The remaining high-quality identical sequences were counted, and the unique sequences with their associated read counts were mapped to the Sino-Danish pig genome assembly (March 2009) [1] by SOAP [2].To identify sequence tags originating from repeats, rRNA, tRNA, snRNA, and snoRNA, we used the Rfam and NCBI GenBank databases. To determine known miRNAs, unique sequences were aligned with porcine precursor miRNA sequences from miRBase (http://microrna.sanger.ac.uk/seguence/index.html; Release13.0, March 2009) with a maximum of two mismatches. Because the current pig genome assembly has imperfect coverage, we performed another blast search against the known human, rat and mouse miRNAs that were deposited in miRBase13.0 to identify the conserved miRNA homologs in pig. Only perfectly matched sequences were considered as conserved miRNAs. To compare the differential expression of miRNAs between the two libraries, the Bayesian method that was developed for the analysis of digital gene expression profiles was used. The number of miRNA read counts in each sample was normalized to the total miRNA read counts.

[1] Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A et al: Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing. Bmc Genomics 2005, 6:70.
[2] Li RQ, Li YR, Kristiansen K, Wang J: SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714.

organism: Sus scrofa

source_name: Whole testis tissue, sexually immature

extract_protocol: For small RNA library construction and deep sequencing, total RNA isolated from the testes of three 30-day-old Junmu-1 boars (sexually immature (I)) and three 180-day-old Junmu-1 boars (sexually mature (M)) were pooled and prepared according to the Solexa EAS Small RNA Sample Prep Protocol. In brief, Solexa sequencing was performed as follows: for each library, approximately 10 Î¼g total RNA extracted by Trizol reagent (Invitrogen) was size-fractionated on a 15% TBE urea denaturing PAGE gel to enrich for molecules in the range of 18-30 nt in length and ligated with proprietary adapters to the 5â²and 3â² termini of the RNA with T4 RNA ligase (Ambion). The adapter-ligated small RNA was converted to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). The resulting cDNA was amplified with 15 PCR cycles using Illuminaâs small RNA primer set. The purified PCR products were quantified on an Agilent Technologies 2100 Bioanalyzer and diluted to 10 nM for sequencing on an Illumina/Solexa 1G Genetic Analyzer at the Beijing Genomics Institute (BGI) (Shenzhen, China) according to the manufacturerâs protocol.

tag: breed

tag: tissue

value: testis

tag: age

value: 30 days

tag: developmental stage

value: sexually immature


title: HVS A11 small RNAs from marmoset T cell infected cj319_A11_WT

status: Public on Sep 21 2011

city: Salt Lake City

first: Demian

middle: E

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

description: RNA of size 18-30 nt

data_processing: Sequencing results were processed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). A total of 12,225,234 quality-filtered reads were aligned to H. saimiri A11 genome (NC_001350) using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml).

organism: Herpesvirus saimiri (strain 11)

source_name: T cells

growth_protocol: Cells were grown in RPMI medium supplemented with 20% FBS and antiobiotics (typically at 2-5 x 106 cells/ml)

extract_protocol: Total RNA was prepared from cells, and small RNAs (18 to 30 nt) were isolated after fractionation in a 15% denaturing polyacrylamide gel.The small RNAs were ligated to a 3  modified linker adapter (miRNA Cloning Linker 1; Integrated DNA Technologies [IDT]), gel purified, and ligated to a 5  RNA adapter (5 -ACACGACGCUCUUCCGAUCU-3 ; IDT). cDNA was synthesized with SuperScript III (Invitrogen) using a DNA primer complementary to the 3  adapter.

tag: sample type

value: Hespesvirus saimiri (strain A11) infected T cell


title: Yale_ChipSeq_MEL_Input_IgG-Yale (superseded by GSM1003747)

description:
****************************
GSM798325 record metadata submitted on Sep 19 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSM1003747
****************************

source_name: MEL

value: Weissman - Yale University

value: ChipSeq

value: ChIP-Seq

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: M

tag: treatment

tag: treatment description

tag: control

tag: control description

tag: age description

tag: controlid

value: MEL/None/Input/IgG-Yale

tag: replicate

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Testis_180 days

data_processing:
Alignment: Raw sequence reads were processed into clean full-length reads using the BGI small RNA pipeline. First, all low-quality reads were removed from the raw sequence, and the 3' adapter reads, 5' adapter contaminants, sequences containing the polyA tail and those smaller than 18 nt were also discarded. The remaining high-quality identical sequences were counted, and the unique sequences with their associated read counts were mapped to the Sino-Danish pig genome assembly (March 2009) [1] by SOAP [2].To identify sequence tags originating from repeats, rRNA, tRNA, snRNA, and snoRNA, we used the Rfam and NCBI GenBank databases. To determine known miRNAs, unique sequences were aligned with porcine precursor miRNA sequences from miRBase (http://microrna.sanger.ac.uk/seguence/index.html; Release13.0, March 2009) with a maximum of two mismatches. Because the current pig genome assembly has imperfect coverage, we performed another blast search against the known human, rat and mouse miRNAs that were deposited in miRBase13.0 to identify the conserved miRNA homologs in pig. Only perfectly matched sequences were considered as conserved miRNAs. To compare the differential expression of miRNAs between the two libraries, the Bayesian method that was developed for the analysis of digital gene expression profiles was used. The number of miRNA read counts in each sample was normalized to the total miRNA read counts.
[1] Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A et al: Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing. Bmc Genomics 2005, 6:70.
[2] Li RQ, Li YR, Kristiansen K, Wang J: SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714.

source_name: Whole testis tissue, sexually mature

value: 180 days

value: sexually mature


title: WT_Flag_leaf_rep1

city: Davis

first: Dario

last: Cantu

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

data_processing: Low quality sequences and vector contaminants were removed using custom scripts available from http://code.google.com/p/atgc-illumina/. High quality reads were aligned with Bowtie to wheat transcripts (454 assembled sequences, TSA project 59945 - accession numbers: HP608076-HP639668)

organism: Triticum aestivum

growth_protocol: Transgenic plants for the NAM RNAi construct  were grown under long-days (LD, 16 h light 8 h dark)

extract_protocol: Amplified cDNA synthesis was performed according to mRNA sequencing protocol  from Illumina (Part # 1004898 Rev. D) and using 10 µg total RNA as starting material

treatment_protocol: At anthesis, spikes were labelled and after 12 days, flag leaves samples from four plants were pooled and used for RNA extraction.

value: flag leaf

tag: genotype/variation

value: wild type

tag: cultivar

value: Bobwhite

tag: Stage

value: 12 Days Post Anthesis


title: GPC_RNAi_Flag_leaf_rep4


title: GPC_RNAi_Flag_leaf_rep3


title: u87_adar_ctrl

first: Gang

last: Li

address: 611 Charles E. Young Drive Rm. 660

institute: UCLA

description: cDNA with control siRNA

data_processing: The sequence reads are aligned to the genome and transcriptome using blat, bowtie and tophat allowing at most 12 mismatches. Unique pair of the alignments of a pair of reads is accepted if both ends have less than 6 mismatches.

source_name: Glioblastoma

growth_protocol: U87MG cells were maintained in DMEM high glucose medium supplemented with pyruvate, L-glutamine, and 10% fetal bovine serum (FBS).

extract_protocol: We used the standard Illumina protocol to prepare libraries for RNA-Seq (http://www.illumina.com/support/documentation.ilmn). Briefly, 10ug total RNA was first processed via poly-A selection and fragmentation. We generated first-strand cDNA using random hexamer-primed reverse transcription and subsequently used it to generate second-strand cDNA using RNase H and DNA polymerase. Sequencing adapters were ligated using the Illumina Paired-End sample prep kit. Fragments of ~200 bp were isolated by gel electrophoresis, amplified by 15 cycles of PCR and sequenced.

treatment_protocol: 50ng of ADAR1 siRNA and control siRNA were transfected respectively with lipofectamine RNAiMAX into 5x104 U87MG cells per single well of 6-well plate via reverse transfection and cells were harvested 48h following transfection. Total RNA was isolated using the RNeasy micro kit.

tag: cell line

value: control siRNA


title: GPC_RNAi_Flag_leaf_rep2

tag: tissue


title: Yale_ChipSeq_MEL_H3K4me3_DMSO_2.0pct_IgG-Yale (superseded by GSM1003754)

description:
****************************
GSM798328 record metadata submitted on Sep 19 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSM1003754
****************************

tag: lab

value: Yale-m

tag: lab description

value: Weissman - Yale University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: 5 d with 2% DMSO (Weissman)

value: IgG-Yale

value: Input signal from Mouse IgG ChIP-seq prepared at Yale

tag: age

value: immortalized

value: Immortal cells

tag: replicate description

value: tier 1