GEO DataSets

(Submitter supplied) Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. We have developed an unbiased genomic method called sequence tag analysis of genomic enrichment (STAGE) to identify the direct binding targets of transcription factors in vivo. STAGE is based on high-throughput sequencing of concatemerized tags derived from target DNA enriched by chromatin immunoprecipitation. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL1485

2 Samples

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(Submitter supplied) To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Keywords: Genome wide map of active chromatin

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3514

4 Samples

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(Submitter supplied) MYC binding sites determined in HeLa cells using ChIP-chip Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3514

3 Samples

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(Submitter supplied) The goal of this study was to map DNaseI sensitivity and DNaseI hypersensitive sites over the ENCODE regions in human lymphoblastoid cells (GM06990, Coriell). Keywords: DNase/Array

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2131

1 Sample

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(Submitter supplied) These are three biological replicates. HeLa cells were crosslinked on separate days. In each case, a matched total from the same crosslinking was produced in parallel. Amplicons were made from each and hybridized onto ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3489

3 Samples

Download data: TXT

(Submitter supplied) BAF170 ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaced every 38bps (overlapping by 12nts). Goal is to identify binding sites for BAF170. Keywords = Transcription Factor Binding, BAF170, ChIP-chip, Human, Genome Tiling Arrays Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2131

4 Samples

Download data: GFF

(Submitter supplied) BAF155 ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaced every 38bps (overlapping by 12nts). Goal is to identify binding sites for BAF155. Keywords = Transcription Factor Binding, BAF155, ChIP-chip, Human, Genome Tiling Arrays Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2131

4 Samples

Download data: GFF

(Submitter supplied) FOS ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify FOS-binding sites. Keywords = Transcription Factor Binding, FOS, ChIP-chip, Human, Genome Tiling Arrays Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2131

3 Samples

Download data: GFF

(Submitter supplied) JUN ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaced every 38bps (overlapping by 12nts). Goal is to identify binding sites for JUN. Keywords = Transcription Factor Binding, JUN, ChIP-chip, Human, Genome Tiling Arrays Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2131

3 Samples

Download data: GFF

(Submitter supplied) Genome-wide location analysis of trimethyl-K4 histone H3 and RNA polymerase II binding in interferon gamma-induced for 30 minutes HeLa cells and uninduced HeLa cells was done using 50mer oligonucletide probes at 38bp intervals tiling over non-repetitive ENCODE regions (HG17, NCBI build 35). Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2533

12 Samples

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(Submitter supplied) Genome-wide location analysis of SUZ12 and TriMeH3K27 binding in HeLa cells (human cervix epithelial adenocarcinoma cells) using RenLab ENCODE PCR tiling array. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1454

6 Samples

Download data: GPR

(Submitter supplied) GWLA analysis of a few promoter and enhancer markers in Hela cells. Keywords: ChIP/chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1454

51 Samples

Download data: GPR, TIFF

(Submitter supplied) STAT1 ChIP-chip performed on Human Hela S3 Cells for three different platforms. Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts) (5 biological replicates), custom maskless array tiling most of ENCODE with 50mer oligonucleotides end-to-end (3 biological replicates) and custom maskless array tiling most of ENCODE with 36mer oligonucleotides end-to-end (2 biological replicates). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL2133 GPL2132 GPL2131

10 Samples

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(Submitter supplied) Transcript Mapping on Affymetrix ENCODE arrays for Total RNA from 4 different samples (2 or 3 technical replicates of each). All of the four same NB4 samples have also been treated with Retanoic Acid (RA) (2 or 3 technical replicates of each). Three of the four same NB4 samples have also been treated with TPA (2 or 3 technical replicates of each). RA treated NB4 cells can be partially differentiated to Neutrophils and TPA treated NB4 cells can be differentiated to Monocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL1789

11 Samples

Download data: CEL

(Submitter supplied) Transcript Mapping on Affymetrix ENCODE arrays for 10 different biological replicates of Neutrophil (PMN) Total RNA (each with 2 technical replicates). Each biological sample is from a different individual. Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL1789

10 Samples

Download data: CEL

(Submitter supplied) Our ability to understand the control logic embedded in the human genome is limited by a lack of accurate information of the promoter sequences for most genes. Promoters are a unique class of control sequences, serving as the binding sites for both sequence-specific factors and the general transcription machinery during transcription initiation. In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex throughout the non-repeat sequences of the human genome in primary fibroblast cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

41 related Platforms

49 Samples

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(Submitter supplied) Transcript Mapping on Affymetrix ENCODE arrays for 3 different biological replicates of Placental Poly(A)+ RNA (each with either 2 or 3 technical replicates) Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL1789

3 Samples

Download data: CEL

(Submitter supplied) ChIP-on-Chip data using histone H3 acetylation antibody and H3K4 methylation antibody. Each in triplicate. Keywords: other

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1454

6 Samples

Download data: TIFF

(Submitter supplied) 2091 mock vs. 2091 E2F4 IP - Human 13K promoter microarray 2091 cells were serum starved for 72hours and fixed with formaldehyde. Keywords: repeat sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1525

2 Samples

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(Submitter supplied) Genome-wide location analysis of TAF1 and RNA polymerase II binding in ENCODE regions of IMR90, HCT116, HeLa and THP1 cell lines. There are a total of 8 experiments, each with three replicates. Details of chromatin immunoprecipitation and data analysis can be found at Li Z, van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B (2003) A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1454

24 Samples

Download data: TIFF, TXT