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TranscriptomicsChromatin immunoprecipitation of human and chimp cell lines GM06990, HFL1, HeLaS3, MOLT4 and PTR8 with anti Histone H3K4me1, H3K4me2, H3K4me3, H3ac and H4ac antibodies using an ENCODE array
ENCODE ChIP/chip study using human lymphoblastoid cell line GM06990; human cervix carcinoma cell line HeLaS3; human fetal lung fibroblast cell line HFL1; human T cell line MOLT4; chimpanzee lymphoblastoid cell line PTR8; and anti Histone H3K4me1 (Abcam; ab8895); H3K4me2 (Abcam; ab7766); H3K4me3 (Abc...
ORGANISM(S): Pan troglodytes 
2006-08-30 | E-TABM-138 | biostudies-arrayexpress
TranscriptomicsGenotyping of human family trios using placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents to find new imprinted genes
Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested using Illumina SNP arrays to find new imprinted genes to ascertain the extent of allele specific expression in this tissue.
ORGANISM(S): Homo sapiens 
2010-04-15 | E-TABM-796 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of mouse embryonic stem cell lines with Dgcr8 mutations to investigate the broad role of miRNAs and individual miRNAs through the reintroduction of miRNA mimics
These experiments were conducted as part of a study to derive the targets of miRNAs. Two independent BayGenomics mouse embryonic stem cell lines (XH157 and XG058), each bearing a gene trap between exons 9 and 10 of the Dgcr8 locus (ENSMUST00000115633, Ensembl v53) were further mutagenised by the tar...
ORGANISM(S): Mus musculus 
2012-08-20 | E-MTAB-418 | biostudies-arrayexpress
GenomicsA SNF2 protein targets variable copy number repeats and thereby influences allele-specific expression
ATRX is an X-linked gene of the SWI/SNF family whose role in vivo is currently unknown. Mutations in ATRX cause syndromal mental retardation. ATRX binds to tandem repeat (TR) sequences both in heterochromatin (e.g. telomeres) and euchromatin. Genes associated with these TRs can be dysregulated when ...
ORGANISM(S): Homo sapiens 
2010-11-02 | E-GEOD-22162 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of REST/NRSF
ENCODE ChIP-chip study using 8 diverse human cell lines; 4 of neural origin (NB69, KELLY, SHSY-5Y, U373) and 4 of non-neural origin (HeLa, HepG2, HEK293 and K562) and anti-REST/NRSF antibody (Santa Cruz Biotech; sc-25398 aka H290) to asses REST-genome interactions across 1% of the human genome used...
ORGANISM(S): Homo sapiens 
2009-03-31 | E-TABM-660 | biostudies-arrayexpress
TranscriptomicsChIP-chip by array of human cells for whole genome profiling of 4 histone modifications
Whole genome profiling of 4 histone modifications (H3K27me1, H3K27me3,H3K36me1 and H3K36me3) using ChIP-on-chip. It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), l...
ORGANISM(S): Homo sapiens 
2010-12-03 | E-MTAB-336 | biostudies-arrayexpress
TranscriptomicsSystematic evaluation of variability in simulated ChIP-chip experiments
The most widely-used method for detecting and measuring genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Many tiling array platforms, amplification methods, and analysis algorithms exist for ChIP-chip, but a rigorous assessment...
ORGANISM(S): Homo sapiens 
2008-01-31 | E-GEOD-9842 | biostudies-arrayexpress
TranscriptomicsChIP-chip by array of human K562, U937 and CD14+ cells to identify histone modifcations in ENCODE regions
Chromatin immunoprecipitation microarray (ChIP-chip) study using 3 human cell lines (K562, U937, CD14+); of 19 histone modifications across 1% of the human genome used in the pilot phase of the ENCODE project.
paper abstract: It has recently been shown that nucleosome distribution, histone modifi...
ORGANISM(S): Homo sapiens 
2010-12-29 | E-MTAB-334 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of human erythroleukemia cell line K-562 with H3K4me2, H3K4me3, H3ac, H4ac, Histone H2B and Histone H3 antibodies using an ENCODE array
ENCODE ChIP-chip study using human myelogenous leukemia cell line K-562 and anti histone H3K4me2 (Abcam; ab7766); H3K4me3 (Abcam; ab8580); H3ac (Upstate; 06-599); H4ac (Upstate; 06-866); Histone H2B (Abcam: ab1790) and Histone H3 (Abcam: ab1791) antibodies. Each antibody experiment was conducted in ...
ORGANISM(S): Homo sapiens 
2006-09-01 | E-TABM-140 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of human lymphoblastic cell line GM06990 using anti Histone H3K4me1, H3K4me2, H3K4me3, H3ac and H4ac antibodies using an ENCODE array
ENCODE ChIP/chip study using lymphoblastic cell line GM06990 and anti Histone H3K4me1, H3K4me2, H3K4me3, H3ac and H4ac antibodies.
ORGANISM(S): Homo sapiens 
2005-06-13 | E-MEXP-269 | biostudies-arrayexpress
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