title: Caltech_ChipSeq_C2C12_Input_Control_32bp

value: Caltech-m

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: Input

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

value: This data represents a control being compared to experiments using read length of 32 bp

value: No special treatment or protocol applies

value: immortalized

tag: labexpid

tag: labversion

value: Myoblast

tag: replicate

tag: strain

tag: strain description


title: Caltech_ChipSeq_C2C12_MyoD_(sc-32758)_Control_50bp_EqS_2.0pct_7d

status: Public on Apr 13 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: lab

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mouse

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

tag: antibody

tag: antibody description

value: mouse monoclonal antibody raised against recombinant MyoD of mouse origin with an epitope mapping to amino acids 180-189. Antibody Target:MyoD

tag: antibody targetdescription

value: This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: control description

value: This data represents a control being compared to experiments using read length of 50 bp

tag: treatment

tag: treatment description

value: 7 d with 2.0% Equine Serum and Insulin (Wold)

tag: age

tag: age description

value: Immortal cells

tag: controlid

value: Myocyte

tag: labversion description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_Myogenin_(sc-12732)_Control_32bp_EqS_2.0pct_60hr

tag: lab

value: Caltech-m

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: mouse monoclonal antibody; epitope mapping within amino acids 138-158 of myogenin of rat origin. Antibody Target:Myogenin

value: Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq)

value: This data represents a control being compared to experiments using read length of 32 bp

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: labexpid

tag: labversion

tag: replicate

tag: strain

tag: strain description


title: Caltech_ChipSeq_C2C12_Myogenin_(sc-12732)_Control_50bp_EqS_2.0pct_7d

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody

tag: antibody description

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: control

tag: control description

value: immortalized


title: Caltech_ChipSeq_C2C12_USF-1_Control_50bp_EqS_2.0pct_60hr

tag: lab

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

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: treatment

tag: treatment description

tag: age

tag: age description

tag: controlid

tag: labversion description


title: Caltech_ChipSeq_C2C12_Input_Control_36bp

tag: lab description

tag: datatype

tag: datatype description

tag: cell sex

tag: antibody

value: Input

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

value: This data represents a control being compared to experiments using read length of 36 bp

value: No special treatment or protocol applies

value: Immortal cells

tag: labexpid

tag: replicate

tag: strain

tag: strain description


title: Caltech_ChipSeq_C2C12_Myogenin_(sc-12732)_Control_32bp_EqS_2.0pct_24hr

tag: lab

value: Caltech-m

tag: cell

tag: cell organism

tag: antibody description

value: mouse monoclonal antibody; epitope mapping within amino acids 138-158 of myogenin of rat origin. Antibody Target:Myogenin

tag: antibody targetdescription

value: Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: control description

value: 24 h with 2.0% Equine Serum and Insulin (Wold)

tag: labversion

value: Myocyte

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_TCF12_Control_50bp_EqS_2.0pct_60hr

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mouse

tag: cell description

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: This data represents a control being compared to experiments using read length of 50 bp

tag: treatment

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

value: immortalized

tag: age description

tag: controlid

tag: labversion description


title: Caltech_ChipSeq_C2C12_USF-1_Control_50bp

tag: lab

tag: cell

tag: cell organism

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

tag: antibody

tag: antibody description

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.

value: No special treatment or protocol applies

value: Immortal cells

tag: labexpid

value: Myoblast

tag: replicate

tag: strain

tag: strain description


title: Ovaries_25d_RH(high capacity to repress)

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: CNRS

description: Small RNAs from reactive female (Cha-R) with aged maternal ancestors

library_source: transcriptomic

data_processing:
RH25d.bonafide_counts.txt; genome build: dm5
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed.
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode, miRNAs from miRBase, transcripts from Flybase and transposable elements from Repbase and from the UCSC repeatmasker track.
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNA, the remainder, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.

molecule: total RNA

organism: Drosophila melanogaster

source_name: 25-day-old ovaries

growth_protocol: Flies were grown at 23 degrees C on standard Drosophila food.

extract_protocol: Extracted small RNAs between 18 and 30 nucleotides were selected on an acrylamide gel and cloned.

treatment_protocol: Small RNAs (18-30nt) were isolated using anion-exchange chromatography extractions.

value: Cha-RL

tag: gender

value: female

tag: tissue

value: ovaries

value: 25 days


title: male-NPCs-E14-replicate-2

status: Public on Apr 11 2012

city: Paris

first: Elphege

middle: Pierre

last: Nora

address: 11-13 rue Pierre et Marie Curie

department: Mammalian developmental epigenetics

institute: Institut Curie

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-NPCs-E14-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

source_name: mES-derived neuronal progenitor cells

growth_protocol: Feeder dependent mESCs (TT2, TT2-G9a 22.10 and XTX) were grown on a mono-layer of mitomycin C treated MEFs and feeder independent mESCs (E14, PGK12.1, EED-l7Rn5-3354SB/l7Rn5-3354SB ,) were grown on gelatin-coated flasks. Culture media consisted in DMEM (Gibco) except for E14 that were grown in Glasgow medium supplemented with 2mM L-Glutamine, 0.1mM NEAA and 1mM sodium pyruvate (Gibco). All mESC media contained 15% FBS (Gibco), 10-4 M b-mercaptoethanol (Sigma), 1000 U/ml of leukaemia inhibitory factor (LIF, Chemicon) and cells were cultivated under 8% CO2. TT2 and  TT2-G9a 22.10. Female heterozygous DXTX cells  were subcloned to isolate an XO line containing only the deleted X chromosome. NPCs were derived in N2B27 (StemCell Sciences) and cultured with N2B27 + 10ng/mL EGF and FGF (Preprotech) on gelatin-coated flasks. Primary MEFs were obtained from E13.5 embryo dissociation (C57BL/6 background) and passaged three times in DMEM containing 10% FBS (Gibco) and 10-4 M b-mercaptoethanol (Sigma).

extract_protocol: 3C DNA was hybridised with a pool of 5C oligonucleotide designed upstream (FORWARD) or downstream (REVERSE) HindIII restriction sites. Ligation of FORWARD and REVERSE oligonucleotides was then performed to generate a 5C library, which was amplified using T3 and T7 primers that hybridise to the respective tails of all 5C-FORWARD and 5C-REVERSE oligonucleotides. 5C libraries were then prepared for paired-end sequencing on a Genome Analyzer II machine according to Illumina's instructions  (Kit PE-102-1001).

tag: cell type

value: mES-derived neuronal progenitor cells

tag: sex chromosome ploidy

value: XY


title: Eggs_0-2hrs_RH(high capacity to repress)

description: Small RNAs from eggs laid by 25 day-old reactive female (Cha-R) with aged maternal ancestors

data_processing:
eRH25d.bonafide_counts.txt; genome build: dm5
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed.
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode, miRNAs from miRBase, transcripts from Flybase and transposable elements from Repbase and from the UCSC repeatmasker track.
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNA, the remainder, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.

source_name: 0-2 hour eggs

value: eggs

tag: age

value: 0-2 hours


title: Ovaries_3d_RL(low capacity to repress)

description: Small RNAs from reactive females (Cha-R) with young maternal ancestors

data_processing:
RL3d.bonafide_counts.txt; genome build: dm5
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed.
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode, miRNAs from miRBase, transcripts from Flybase and transposable elements from Repbase and from the UCSC repeatmasker track.
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNA, the remainder, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.

source_name: 3-day-old ovaries

value: 3 days


title: male-NPCs-E14-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-NPCs-E14-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: male-mESCs-TT2-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-TT2-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

source_name: Undifferentiated mouse embryonic stem cells


title: Ovaries_3d_SFL(low capacity to repress)

description: Small RNAs from female progeny of a cross between Cha-RL female (reactive female with young maternal ancestors) and Cha-I male.

data_processing:
SFL3d.bonafide_counts.txt; genome build: dm5
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed.
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode, miRNAs from miRBase, transcripts from Flybase and transposable elements from Repbase and from the UCSC repeatmasker track.
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNA, the remainder, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.

value: Cha-RL x Cha-I


title: male-mESCs-TT2-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-TT2-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

value: Undifferentiated mouse embryonic stem cells


title: Ovaries_3d_RH(high capacity to repress)

description: Small RNAs from reactive females (Cha-R) with aged maternal ancestors

data_processing:
RH3d.bonafide_counts.txt; genome build: dm5
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed.
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode, miRNAs from miRBase, transcripts from Flybase and transposable elements from Repbase and from the UCSC repeatmasker track.
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNA, the remainder, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.


title: male-mESCs-TT2-G9Aminus-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-TT2-G9Aminus-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: male-mESCs-TT2-G9Aminus-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-TT2-G9Aminus-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: male-mESCs-EEDminus-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-EEDminus-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: male-mESCs-E14-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-E14-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: male-mESCs-E14-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-E14-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: femaleXO-mESCs-DXTX-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
femaleXO-mESCs-DXTX-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

value: XO


title: femaleXO-mESCs-DXTX-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
femaleXO-mESCs-DXTX-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: male-mESCs-day-2-E14-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-day-2-E14-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

source_name: mouse embryonic stem cells differentiated for two days with retinoic acid


title: male-mESCs-day-2-E14-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-day-2-E14-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

value: mouse embryonic stem cells differentiated for two days with retinoic acid


title: female-mESCs-PGK12.1-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
female-mESCs-PGK12.1-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

value: XX


title: female-mESCs-PGK12.1-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
female-mESCs-PGK12.1-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: Ovaries_3d_SFH(high capacity to repress)

description: Small RNAs from female progeny of a cross between Cha-RL female (reactive female with aged maternal ancestors) and Cha-I male.

data_processing:
SFH3d.bonafide_counts.txt; genome build: dm5
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed.
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode, miRNAs from miRBase, transcripts from Flybase and transposable elements from Repbase and from the UCSC repeatmasker track.
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNA, the remainder, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.


title: female-mESCs-day-2-PGK12.1-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
female-mESCs-day-2-PGK12.1-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly


title: female-MEFs-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
female-MEFs-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

source_name: Primary mouse fibroblasts derived from E13.5 embryos


title: female-MEFs-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
female-MEFs-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

value: Primary mouse fibroblasts derived from E13.5 embryos


title: cisplatin_resistant_cell line_MDB-Seq

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

country: China

institute: ZheJiang University

data_processing: Peak detected by software MEDIPS (http://medips.molgen.mpg.de/), Alignment: Sequence reads were obtained and trimmed into 35bp then mapped to the hg19 genomes using the SOAP2. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 500 bp to create summary windows.

organism: Homo sapiens

source_name: cisplatin resistant cell line

extract_protocol: DNA isolated was sheared to ~300 bp using the sonicator and size separated by PAGE (8%). The 200-400bp DNA fraction was excised, eluted overnight at 4°C in 200µl of elution buffer and purified using a purification kit. The size selected DNA was end-repaired, A-tailed, and ligated to 2.5mMol of "paired-end" adapters (IDT Inc.) following the manufactures recommend protocol (Ilumina Inc.). The resulting product was purified on a QiaquickMinElute column (Qiagen, Mississauga, Ontario) and assessed and quantified using an Agilent DNA 1000 series II assay and Qubitfluorometer (Invitrogen, Carlsbad, CA) respectively. 100ng of pre-adapted, size selected product was subjected to immunoprecipitation using the MethylMinerMethylated DNA Enrichment Kit (Invitrogen) following the manufactures recommended protocol. The bound fraction was eluted at 600mM, 1M and 2M NaCl and concentrated by the addition of 1µl (20ug/ul) mussel glycogen, 1/10th v/v 3M sodium acetate (pH5.2) and 2x v/v 100% ethanol. Samples were incubated at -80°C for 2 hours and subsequently centrifuged for 15 minutes at 14,000rpm at 4°C. Pellets were washed with 500µl cold 70% ethanol 2 times with 5 minute centrifugation at 14,000rpm at 4°C between washes and re-suspended in 60µl nuclease-free water. Following purification eluted products were subjected to PCR using Illumina paired-end adapters (Illumina Inc.) with 15 cycles of PCR amplification.

tag: cell line

value: ovarian cancer cell line

value: 5-methylcytidine antibody


title: cisplatin_sensitive_cell line_MDB-Seq

source_name: cisplatin sensitive cell line


title: control treatment mRNA degradome seq

city: Wuhan

first: Zhonghui

last: Tang

address: Huazhong Agricultural University

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by BGI mRNA degradome analysis pipeline
Genome_build: Triticum aestivum: UniGene Build #59
Supplementary_files_format_and_content: tab-delimited text files include mRNA tag length, mRNA tag frequency and mRNA tag sequence

molecule: polyA RNA

organism: Triticum aestivum

source_name: spike tissue

extract_protocol: We analyzed spikes from anthers at three developmental stages (including the T0 stage): 1.5-mm anthers in which secondary sporogenous cells were formed; 2.2-mm anthers in which all cell layers were present and mitosis had ceased; and 3.0-mm anthers at the meiotic division stage. To maximize the morphological synchronicity of samples at each individual stage, approximately 20 spikes were collected from primary stems at each stage. The spikes at corresponding stages were also harvested from stems of plants kept in control conditions, using leaf age index and anther length as guide. Total RNAs were isolated from spike tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. After total RNA isolation, RNAs from cold-treated and control spike tissues were mixed, respectively. mRNA degradome libraries were constructed following the instructions of the manufacturer.

value: spikes

tag: developmental stage

value: anthers of 1.5 to 3.0 mm in  length

tag: treatment

value: Control

value: thermosensitive genic male sterile (TGMS) line


title: Stanford_ChipSeq_MEL_c-Myc_IgG-rab

source_name: MEL

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: M

value: c-Myc

tag: antibody antibodydescription

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

tag: antibody targetdescription

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

value: MEL/None/Input/IgG-rab

value: Unknown

value: Unknown strain origin


title: Yale_ChipSeq_MEL_Input_DMSO_2.0pct_IgG-Yale

value: Yale-m

value: Weissman - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

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.

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

value: IgG-Yale

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

tag: age

tag: strain

tag: strain description


title: Stanford_ChipSeq_CH12_SMC3_(ab9263)_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: Rabbit polyclonal raised against synthetic peptide representing a portion within the last 100 amino acids of the human Structural Maintenance of Chromosomes-3 conjugated to KLH. Antibody Target:SMC3

value: Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex.  The cohesin complex is required for the cohesion of sister chromatids after DNA replication.

value: Abcam

tag: treatment

value: No special treatment or protocol applies

tag: replicate

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


title: Stanford_ChipSeq_MEL_NELFe_IgG-rab

value: ChipSeq

value: MEL

value: Leukemia (K562 analog)

value: M

value: NELFe

tag: antibody antibodydescription

value: NELFe (RDBP). Antibody Target:NELFe

tag: antibody targetdescription

value: NELFe (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: treatment description

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: immortalized

tag: age description

value: Immortal cells

value: MEL/None/Input/IgG-rab

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_Rad21_DMSO_2.0pct_IgG-rab

value: Stanford-m

value: Snyder - Stanford University

value: Chromatin IP Sequencing

tag: cell organism

value: mouse

tag: cell sex

tag: antibody

value: Rabbit polyclonal. Antibody Target:RAD21

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

value: Abcam

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: age

tag: controlid

tag: strain

tag: strain description


title: Stanford_ChipSeq_MEL_Rad21_IgG-rab

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

value: MEL

tag: cell description

value: Leukemia (K562 analog)

value: M

tag: treatment

value: No special treatment or protocol applies


title: cold treatment mRNA degradome seq

tag: tissue

value: spikes

tag: developmental stage

value: anthers of 1.5 to 3.0 mm in  length

value: Cold treatment

value: thermosensitive genic male sterile (TGMS) line


title: Stanford_ChipSeq_MEL_Mxi1_(AF4185)_IgG-rab

value: Stanford-m

tag: antibody antibodydescription

value: Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target:Mxi1

tag: antibody targetdescription

value: Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX

tag: antibody vendorname

value: R&D Systems

tag: antibody vendorid

tag: treatment description

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: immortalized

tag: age description

value: Immortal cells

value: MEL/None/Input/IgG-rab

tag: replicate

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_CHD2_(AB68301)_IgG-rab

tag: lab

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: MEL

tag: cell organism

value: mouse

value: Leukemia (K562 analog)

tag: cell sex

value: M

tag: antibody

value: Rabbit polyclonal to CHD2 Synthetic peptide derived from within residues 1250 - 1350 of Human CHD2. Antibody Target:CHD2

value: CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template.

value: Abcam

tag: age

tag: controlid

tag: strain

tag: strain description


title: male-mESCs-EEDminus-replicate-2

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-mESCs-EEDminus-replicate-2.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

tag: cell type

value: Undifferentiated mouse embryonic stem cells

tag: sex chromosome ploidy

value: XY


title: male-MEFs-replicate-1

description: ligated DNA oligonuclotides

data_processing:
mapping: each side of the paired end read, which were independently mapped to a pseudo-genome of all possible 5C oligonucleotides sequences using the novoalign mapping algorithm (V2.05 http://novocraft.com) with default settings. After mapping, if both of the paired end reads could be uniquely mapped to a 5C primer, a 5C interaction was assembled. Invalid interactions between the same primer or between primers of the same type were removed as these would represent a mapping artifact or an issue with the 5C technique.
Some 5C oligonucleotides were found to show artifactual ligation patterns (e.g. constitutively high signal or no signal at all) and were therefore flagged as outliers and removed from the analysis. As oligonucleotide was flagged as outlier if its median interaction count was 2.5 times higher than the interquartile range of the median counts of the whole oligonucleotide set in at least half of the experiments. Median counts were computed using primers that had non-null count values.
Genome Build:
male-MEFs-replicate-1.matrix: Mapping was done on a virtual genome made of all possible 5C oligonucleotide ligation products. Coordinates of FORWARD and REVERSE oligonucleotides are based on mm9 assembly

value: Primary mouse fibroblasts derived from E13.5 embryos


title: Stanford_ChipSeq_CH12_Mxi1_(AF4185)_IgG-rab

value: Stanford-m

tag: datatype

tag: datatype description

tag: cell

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody antibodydescription

value: Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target:Mxi1

tag: antibody targetdescription

value: Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX

tag: antibody vendorname

value: R&D Systems

tag: antibody vendorid

tag: treatment

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: immortalized

value: Immortal cells

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


title: Stanford_ChipSeq_CH12_Pol2(phosphoS2)_IgG-rab

tag: lab

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: mouse

tag: cell sex

value: Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target:POL2S2

value: RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain.

tag: treatment description

tag: control

tag: control description

tag: age description

tag: replicate


title: Stanford_ChipSeq_MEL_SMC3_(ab9263)_IgG-rab

value: Stanford-m

tag: datatype

tag: datatype description

value: MEL

value: Leukemia (K562 analog)

value: M

tag: antibody

value: Rabbit polyclonal raised against synthetic peptide representing a portion within the last 100 amino acids of the human Structural Maintenance of Chromosomes-3 conjugated to KLH. Antibody Target:SMC3

value: Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex.  The cohesin complex is required for the cohesion of sister chromatids after DNA replication.

value: Abcam

tag: age

tag: controlid

value: MEL/None/Input/IgG-rab

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Stanford_ChipSeq_CH12_NELFe_IgG-rab

tag: cell

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: NELFe

tag: antibody antibodydescription

value: NELFe (RDBP). Antibody Target:NELFe

tag: antibody targetdescription

value: NELFe (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: treatment

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: immortalized

value: Immortal cells

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


title: Stanford_ChipSeq_CH12_p300_(SC-584)_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: mouse

tag: cell sex

value: Rabbit polyclonal IgG, epitope mapping at the N-terminus of p300 of human origin. Antibody Target:P300

value: Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein

tag: treatment description

tag: control

tag: control description


title: Stanford_ChipSeq_MEL_Max_IgG-rab

tag: datatype

tag: datatype description

value: MEL

value: Leukemia (K562 analog)

value: M

tag: antibody

value: Max

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

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

tag: age

tag: age description

tag: controlid

value: MEL/None/Input/IgG-rab

tag: replicate

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_CH12_Input_IgG-mus

tag: cell

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: Input

tag: antibody description

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

value: No special treatment or protocol applies

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

value: immortalized

value: Immortal cells

tag: strain

tag: strain description

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


title: Stanford_ChipSeq_MEL_Input_std

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: MEL

tag: cell organism

value: mouse

value: Leukemia (K562 analog)

value: M

tag: treatment

value: std

value: Standard input signal for most experiments.

value: MEL/None/Input/std


title: Stanford_ChipSeq_MEL_p300_IgG-rab

tag: cell sex

tag: antibody antibodydescription

value: Rabbit Polyclonal. Antibody Target:P300

tag: antibody targetdescription

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: MEL/None/Input/IgG-rab

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_E2F4_IgG-rab

value: Stanford-m

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

tag: antibody

value: rabbit polyclonal. Antibody Target:E2F4

value: mapping at the C-terminus of E2F4 of human origin

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: replicate


title: Stanford_ChipSeq_CH12_BHLHE40_(NB100-1800)_IgG-rab

tag: lab

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: Rabbit polyclonal, maps to a region between residues 350 and the C-terminus (residue 412). Antibody Target:BHLHE40

value: This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation.

value: Novus

tag: treatment

tag: strain

tag: strain description

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


title: Stanford_ChipSeq_MEL_JunD_IgG-rab

value: MEL

value: Leukemia (K562 analog)

tag: cell sex

value: M

value: JunD

tag: antibody antibodydescription

value: rabbit polyclonal IgG. Antibody Target:JunD

tag: antibody targetdescription

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

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: MEL/None/Input/IgG-rab

value: Unknown


title: Stanford_ChipSeq_CH12_E2F4_IgG-rab

value: Stanford-m

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: mouse

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody

value: rabbit polyclonal. Antibody Target:E2F4

value: mapping at the C-terminus of E2F4 of human origin

tag: control description

tag: age

value: immortalized

tag: age description

value: Immortal cells


title: Stanford_ChipSeq_MEL_Pol2(phosphoS2)_IgG-rab

tag: lab

tag: lab description

value: MEL

tag: cell organism

tag: cell description

value: Leukemia (K562 analog)

value: M

value: Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target:POL2S2

value: RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain.

value: Abcam

tag: treatment

tag: controlid

tag: replicate

value: Unknown strain origin


title: Stanford_ChipSeq_CH12_CTCF_(SC-15914)_IgG-rab

value: Stanford-m

value: Snyder - Stanford University

tag: cell sex

tag: antibody antibodydescription

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

tag: antibody targetdescription

value: Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: strain

tag: strain description

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


title: Stanford_ChipSeq_CH12_USF2_IgG-mus

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: mouse

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody

value: Mouse monoclonal. Immunogen corresponds to amino acids 1-101 of Human USF2. Antibody Target:USF2

value: Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3').

value: abcam

tag: treatment description

tag: control

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

value: immortalized

value: Immortal cells


title: Stanford_ChipSeq_CH12_Rad21_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: cell organism

tag: cell description

value: Rabbit polyclonal. Antibody Target:RAD21

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

value: Abcam

tag: treatment

tag: age

tag: age description


title: Stanford_ChipSeq_CH12_CHD2_(AB68301)_IgG-rab

value: ChipSeq

tag: cell sex

tag: antibody antibodydescription

value: Rabbit polyclonal to CHD2 Synthetic peptide derived from within residues 1250 - 1350 of Human CHD2. Antibody Target:CHD2

tag: antibody targetdescription

value: CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template.

tag: antibody vendorname

tag: antibody vendorid

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid

tag: replicate

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


title: Stanford_ChipSeq_MEL_c-Myb_(SC-7874)_IgG-rab

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: M

tag: antibody

value: Rabbit polyclonal IgG, Epitope corresponding to amino acids 500-640 mapping at the C-terminus of c-Myb of human origin. Antibody Target:c-Myb

value: Transcriptional activator; DNA-binding protein that specifically recognize the sequence 5'-YAAC[GT]G-3'. Plays an important role in the control of proliferation and differentiation of hematopoietic progenitor cells.

value: Santa Cruz Biotech

tag: treatment description

value: MEL/None/Input/IgG-rab

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_Input_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

tag: cell organism

tag: cell description

value: Input

tag: antibody description

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

tag: treatment

tag: control

tag: control description

value: immortalized

value: Immortal cells


title: Stanford_ChipSeq_CH12_c-Jun_IgG-rab

value: Chromatin IP Sequencing

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

value: c-Jun

tag: antibody antibodydescription

value: Rabbit polyclonal to amino acids 1-79 mapping at the N-terminus of c-Jun p39 of human origin. Antibody Target:c-Jun

tag: antibody targetdescription

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

tag: antibody vendorname

tag: antibody vendorid

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age

tag: age description

tag: controlid

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


title: Stanford_ChipSeq_MEL_GATA-1_IgG-rat

value: Stanford-m

tag: datatype

tag: datatype description

tag: cell

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: M

tag: antibody

value: Anti-GATA-1 rabbit polyclonal antibody was generated by using a purified GST fusion to amino acids 1-89 of mouse GATA-1. Antibody Target:GATA1

value: GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells.

value: Donated by Dr. E.H. Bresnick, UW Madison

tag: treatment description

value: IgG-rat

value: Input signal from Normal Rat IgG ChIP-seq

value: MEL/None/Input/IgG-rat

tag: replicate

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_Input_IgG-mus

tag: lab

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

tag: cell description

value: Input

tag: antibody description

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

tag: treatment

value: No special treatment or protocol applies

tag: control

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

value: immortalized

value: Immortal cells

value: MEL/None/Input/IgG-mus


title: Stanford_ChipSeq_CH12_MafK_(ab50322)_IgG-rab

value: Stanford-m

value: mouse

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: antibody antibodydescription

value: Rabbit polyclonal. Raised against synthetic peptide:TTNPKPNKALKVKKEA conjugated to KLH by a C-terminal Cysteine residue linker, corresponding to amino acids 2-17 of Human MAFK. Antibody Target:MafK

tag: antibody targetdescription

value: NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age

tag: age description

tag: controlid

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


title: Stanford_ChipSeq_CH12_Max_IgG-rab

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: antibody

value: Max

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

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

value: Santa Cruz Biotech

tag: treatment description

tag: replicate

tag: strain

tag: strain description


title: Stanford_ChipSeq_CH12_JunD_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

tag: cell organism

tag: cell description

value: JunD

value: rabbit polyclonal IgG. Antibody Target:JunD

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

tag: treatment

value: No special treatment or protocol applies

tag: control

tag: control description

value: immortalized

value: Immortal cells


title: Yale_ChipSeq_MEL_Input_DMSO_2.0pct_std

value: Yale-m

value: Weissman - Yale University

value: MEL

value: mouse

value: Leukemia (K562 analog)

tag: cell sex

value: M

value: Input

tag: antibody description

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

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

value: std

value: Standard input signal for most experiments.

tag: age

tag: age description

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_MafK_(ab50322)_IgG-rab

value: Stanford-m

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: antibody antibodydescription

value: Rabbit polyclonal. Raised against synthetic peptide:TTNPKPNKALKVKKEA conjugated to KLH by a C-terminal Cysteine residue linker, corresponding to amino acids 2-17 of Human MAFK. Antibody Target:MafK

tag: antibody targetdescription

value: NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid

value: MEL/None/Input/IgG-rab


title: Stanford_ChipSeq_MEL_Input_IgG-rat

tag: lab

tag: lab description

value: MEL

tag: cell organism

value: mouse

value: Leukemia (K562 analog)

value: M

tag: antibody

value: Input

tag: treatment description

value: No special treatment or protocol applies

value: IgG-rat

value: Input signal from Normal Rat IgG ChIP-seq

value: immortalized

value: Immortal cells

value: MEL/None/Input/IgG-rat

tag: replicate

tag: strain

tag: strain description


title: Stanford_ChipSeq_MEL_Pol2_IgG-mus

value: Stanford-m

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

tag: cell sex

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

value: RNA Polymerase II

value: Covance

tag: treatment

tag: control

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: age

tag: age description

value: MEL/None/Input/IgG-mus

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_CTCF_(SC-15914)_IgG-rab

tag: datatype

tag: datatype description

tag: cell

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: M

tag: antibody antibodydescription

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

tag: antibody targetdescription

value: Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: MEL/None/Input/IgG-rab


title: Stanford_ChipSeq_CH12_Pol2_IgG-mus

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody

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

value: RNA Polymerase II

value: Covance

tag: treatment description

value: immortalized

value: Immortal cells

tag: controlid

tag: replicate

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


title: Stanford_ChipSeq_CH12_TBP_IgG-mus

value: mouse

tag: cell description

tag: cell sex

value: TBP

value: Mouse monoclonal. Immunogen is synthetic peptide conjugated to KLH derived from within residues 1 - 100 of HumanTATA binding protein TBP. Antibody Target:TBP

value: General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription.

value: abcam

tag: treatment

tag: control

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: strain

tag: strain description


title: Stanford_ChipSeq_MEL_TBP_IgG-mus

value: Stanford-m

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

value: MEL

value: Leukemia (K562 analog)

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

value: No special treatment or protocol applies

tag: age

tag: age description

value: MEL/None/Input/IgG-mus

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_USF2_IgG-mus

tag: lab

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

value: mouse

tag: antibody

value: Mouse monoclonal. Immunogen corresponds to amino acids 1-101 of Human USF2. Antibody Target:USF2

value: Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3').

tag: antibody vendorname

tag: antibody vendorid

tag: treatment description

value: immortalized

value: Immortal cells


title: 750 ppm 3

status: Public on Apr 10 2012

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

description: Primary polyps at 750 ppm

data_processing: Data were mapped to the Acropora millepora transcriptome using bowtie v0.12.7, allowing up to 2 mismatches. Reads mapping to more than 10 references were discarded. GSM*.counts.txt supplementary files list TSA assembly accession numbers and counts.

organism: Acropora millepora

source_name: Primary polyps at 750 ppm

growth_protocol: Fifteen adult colonies of Acropora millepora were collected off the coast of Orpheus Island, Queensland, Australia (GBRMPA Permit No G10/33232.1), prior to the spawning event in November, 2009 and transported to the aquaculture facilities at James Cook University in Townsville where they were maintained in outdoor flow-through aquaria filled with 5 μm filtered seawater.

extract_protocol: Total RNA was extracted from the samples using Trizol Reagent (Invitrogen) and dissolved in RNAse free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrometer and denaturing gel electrophoresis. Before being shipped on dry ice to the Macrogen sequencing facilities in Seoul, South Korea, each RNA sample was precipitated in ethanol and sodium-acetate (2x and 0.1x sample volume respectively), and stored at -80°C.

treatment_protocol: Larvae were cultivated and settled under ambient conditions (380 ppm pCO2(air), pH 8.16 ± 0.01, 27.5°C). Five days after fertilization, settlement was induced by placing autoclaved unglazed terracotta tiles treated with crustose coralline algae into the container holding the larvae.  Twenty-four hours after the induction of settlement, tiles on which Acropora millepora primary polyps settled were transferred to the experimental tanks, where they were exposed for 3 days to seawater that had been equilibrated with air containing 380 ppm (pH~8.16), 750 ppm (pH~7.96), or 1000 ppm CO2 (pH~7.86)

tag: developmental stage

value: primary polyp

tag: treatment

value: 750 ppm

tag: tissue

value: whole polyps


title: 1000 ppm 1

description: Primary polyps at 1000 ppm

source_name: Primary polyps at 1000 ppm


title: 750 ppm 2

description: Primary polyps at 750 ppm


title: 1000 ppm 2

description: Primary polyps at 1000 ppm


title: 750 ppm 1

description: Primary polyps at 750 ppm


title: Stanford_ChipSeq_CH12_c-Myc_IgG-rab

value: Stanford-m

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: Santa Cruz Biotech

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid

tag: replicate

tag: strain

tag: strain description

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


title: Control 3

description: Primary polyps at 380 ppm

source_name: Primary polyps at 380 ppm

value: 380 ppm (control)


title: RenLab-HiC-cortex, replicate one

city: La Jolla

first: Feng

last: Yue

address: 9500 Gilman Dr.

institute: Ludwig Institue for Cancer Research

description: equivalent to Sample GSM938750

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
cortex_HindIII_ori_HiC.nodup.hic.summary.txt: mm9

source_name: Mouse ES

growth_protocol: mESC line J1 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments. H1 and IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91

extract_protocol: Hi-C experiment were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

value: cortex

tag: restriction enzyme

value: HindIII


title: RenLab-HiC-cortex, replicate two

description: equivalent to Sample GSM938751

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
cortex_HindIII_replicate_Hic.nodup.hic.summary.txt: mm9


title: Control 1

description: Primary polyps at 380 ppm

value: primary polyp


title: Stanford_ChipSeq_MEL_p300_(SC-584)_IgG-rab

tag: lab

tag: lab description

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

value: mouse

value: Leukemia (K562 analog)

value: M

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal IgG, epitope mapping at the N-terminus of p300 of human origin. Antibody Target:P300

tag: antibody targetdescription

value: Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein

value: No special treatment or protocol applies

tag: age

value: immortalized

tag: age description

value: Immortal cells

value: MEL/None/Input/IgG-rab

value: Unknown

value: Unknown strain origin


title: RenLab-HiC-hESC, replicate two

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
hESC_HindIII_HiC_replicate.nodup.hic.summary.txt: hg18

source_name: Human ES

tag: cell line

value: hESC line H1


title: RenLab-HiC-IMR90, replicate two

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
IMR90_HindIII_HiC_replicate.nodup.hic.summary.txt: hg18

source_name: Human IMR90

value: IMR90 fetal lung fibroblast cell line


title: RenLab-HiC-hESC, replicate one

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
hESC_HindIII_HiC.nodup.summary.txt: hg18

value: HindIII


title: 1000 ppm 3

description: Primary polyps at 1000 ppm

tag: developmental stage

value: primary polyp

tag: treatment

tag: tissue

value: whole polyps


title: RenLab-HiC-mESC-NCoI

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
J1_mESC_NcoI_HiC.nodup.summary.txt: mm9

tag: strain

value: mESC line J1

value: NcoI


title: Nkx3-1_HET1_ChIP-Seq

status: Public on Apr 09 2012

city: Nashville

first: Philip

middle: D

last: Anderson

state: TN

department: Pathology

institute: Vanderbilt University

data_processing:
Reads were mapped to HS37.1 with no more than 2 mismatches tolerated. WT and HET samples were normalized by KO. MACS was used to call peaks and output bed files.
Genome Build:
Nkx3-1_HET1_peaks.bed: NCBI 37.1

extract_protocol: Whole prostates from Nkx3.1+/+, Nkx3.1+/- and Nkx3.1-/- mice at 12-16 weeks of age were used. Initial ChIP using anti-Nkx3.1 antibody (Santa Cruz Biotechnology, sc-15022,) was performed by GenPathway. HudsonAlpha performed deep sequencing. The genome coordinates of each read was inferred based on sequence homology to mouse genome build 37. Peaks were called using the Model Based Analysis of ChIP-Seq (MACS) algorithm {Zhang, 2008 #493} using the KO sample as a control for nonspecific Nkx3.1 antibody binding.

value: Recombinant inbred B6 x 129

tag: sac age (wks)

value: whole prostate

tag: genotype/variation

value: anti-Nkx3.1 (Santa Cruz Biotechnology, sc-15022)


title: Nkx3-1_WT1_ChIP-Seq

data_processing:
Reads were mapped to HS37.1 with no more than 2 mismatches tolerated. WT and HET samples were normalized by KO. MACS was used to call peaks and output bed files.
Genome Build:
Nkx3-1_WT1_peaks.bed: NCBI 37.1


title: Nkx3-1_KO_ChIP-Seq

data_processing:
Reads were mapped to HS37.1 with no more than 2 mismatches tolerated. WT and HET samples were normalized by KO. MACS was used to call peaks and output bed files.
Genome Build:
Nkx3-1_KO_peaks.bed: NCBI 37.1


title: Nkx3-1_WT2_ChIP-Seq

data_processing:
Reads were mapped to HS37.1 with no more than 2 mismatches tolerated. WT and HET samples were normalized by KO. MACS was used to call peaks and output bed files.
Genome Build:
Nkx3-1_WT2_peaks.bed: NCBI 37.1


title: Nkx3-1_HET2_ChIP-Seq

data_processing:
Reads were mapped to HS37.1 with no more than 2 mismatches tolerated. WT and HET samples were normalized by KO. MACS was used to call peaks and output bed files.
Genome Build:
Nkx3-1_HET2_peaks.bed: NCBI 37.1


title: WT 1h E2 ER alpha ChIP-seq

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

description: WT_E2 ER

data_processing:
Sequences (36 nt reads) were aligned to the mouse genome (NCBI Build 37.1/mm9) using Eland (Illumina pipeline) software. Only unique genomic hits with no more than 2 mismatches were retained. The Partek Genomics Suite (Partek Inc, St Louis, MO) was used for detection of ERα peaks. Peaks were then filtered using intra- and inter- sample statistics, with a binomial test between sample and control, a Mann-Whitney U test for the separation of forward and reserve reads, and application of FDR cut off of  0.05.  For coverage files, mapped reads were extended to the average fragment length for the given sample and converted to bedGraph format.
Genome Build:
WT_E2.ER_peaks.bed: mm9
WT_E2.fragsize140.bedGraph.gz: mm9

source_name: uterus

growth_protocol: mice were maintained on NIH-31 chow, standard light/dark cycle, 1-5 mice per cage

extract_protocol: Uteri were submersed in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearor (Biospec Products, Bartlesville, OK) and finally spun down and washed 2x in PBS. Chromatin was isolated from the sample by adding 5-10 ml lysis buffer containing PIPES, Igepal, PMSF and Protease Inhibitor Cocktail, followed by disruption with a Dounce homogenizer. Samples were pelleted by centrifugation and resuspended in buffer containing Na deoxycholate, SDS, and Triton X-100. Lysates were sonicated using a Misonix Sonicator 3000 (Misonix, Farmingdale, NY) equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and the chromatin suspensions were transferred to new tubes and stored at -80 C. To prepare Input DNA (genomic DNA), two aliquots of 10-25 µl each (approximately 1/50 of each chromatin preparation) were removed and treated with RNase for 1-2 h at 37 C, proteinase K for 3 h at 37 C, and 65 C heat for at least 6 h to overnight for de-crosslinking. DNAs were purified by phenol-chloroform extraction and ethanol precipitated. Pellets were resuspended in 1/5 TE. Resulting DNAs were quantified on a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE). Extrapolation to the original chromatin volume allowed determination of the yield for each chromatin preparation, as measured by the DNA content.  Prior to use in ChIP, protein A agarose beads (Invitrogen Technologies, Carlsbad, CA) were preblocked using blocking proteins and nucleic acids for 3 h. For each ChIP reaction, an aliquot of chromatin (20-30 µg) was precleared with 30 µl preblocked protein A agarose beads for 1-2 h. ChIP reactions were set up using precleared chromatin and antibody to ERα (sc-542, Santa Cruz Inc, Santa Cruz CA) or PolII phospho Ser5 (ab5095, Abcam, Cambridge, MA) in a buffer containing Na deoxycholate and incubated overnight at 4 C. Preblocked protein A agarose beads were added and incubation at 4 C was continued for another 3 h. Agarose beads containing the immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. An SDS-containing buffer was added to elute the immune complexes from the beads, and the eluates were subjected to RNase treatment at 37 C for 20 min and proteinase K treatment at 37 C for 3 h. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNAs were purified by phenol/chloroform extraction and ethanol precipitation. Quality of ERα ChIP enrichment was assayed by qPCR using primers against candidate EREs in the Igf1 and Stat5a promoters (9). Quality of PolII ChIP enrichment was assayed by qPCR using primers against region in Intron 1 of the housekeeping genes Actin B and  Gapdh. Input DNA was queried at the same sites in parallel. ChIP DNA was amplified by following the Illumina ChIP-Seq DNA Sample Prep Kit (Illumina, Inc.  San Diego, California)  protocol. In brief, DNA ends were polished and 5’-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-A to the ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size fractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles, Phusion polymerase, New England Bioloabs, Ipswich, MA), the resulting DNA libraries were quantified and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions. DNA libraries were sequenced on a Genome Analyzer II (Illumina).

treatment_protocol: mice were ovariectomized and injected intraperitoneally 10-14 days later with saline vehicle or estradiol (250 ng/mouse). Uterine tissue was collected one hour later

value: uterus

tag: agent

value: estradiol

tag: chip antibody

value: ER alpha (sc-542, lot# D1310, Santa Cruz)


title: H3K4me3_MLL2_KO_LPS_4h

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin IP against H3K4me3

data_processing: Alignment: sequence reads were mapped to the mouse mm9 genome using Bowtie (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.

growth_protocol: Bone marrow cells isolated from mixed C57BL/6 (94%) and 129/Ola (6%) mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% Î²-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65C. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for Solexa 2G sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturerâs instruction.

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS, 10 ug/ml)

tag: strain background

tag: cell type

value: Primary BMDM cells (7th day of differentiation)

value: Anti- Histone H3 trimethyl Lys4 (Active Motif, Catolog # 39159)

value: LPS (10 ug/ml) for 4hrs