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Series GSE63434 Query DataSets for GSE63434
Status Public on Mar 21, 2020
Title Kdm5b depletion in embryonic stem cells does not induce intragenic promoters or affect transcription [HELP-tagging]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary The application of massively-parallel sequencing (MPS) technology to understanding how the genome is regulated is of major importance, as we now appreciate sequence variants associated with common heritable diseases to be enriched at regulatory elements in the genome. There is, however, an enormous challenge inherent to these studies, which are much more varied as assays and in terms of analytical approaches than the approaches  used to define the sequence variants themselves. For example, there areis a plethora of assays that test 5-methylcytosine genome-wide, numerous different analytical approaches to defineing peaks from chromatin immunoprecipitation sequencing (ChIP-seq), and increasingly diverse aspects of genomic regulation being studied. The extremely large data sets generated do not lend themselves to distribution without some degree of pre-processing, and the hardware requirements for running these analyses are often substantial. We have highlighted these concerns previously, but the central concern for our field is that genomics research is especially prone to poor reproducibility, and is a prime candidate for implementation of measures that could help to address this general problem.To illustrate the practical issues involved in genomics reproducibility, we sought to analyze our and three previoulsy published studies of the histone demethylase KDM5B using the same analytical approaches.
Overall design Cytosine methylation profile of mouse embryonic stem (mES) cells after knock down of Kdm5b
Contributor(s) Ramos M, Johnston AD, Greally JM
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Submission date Nov 18, 2014
Last update date Mar 22, 2020
Contact name Andrew Johnston
Organization name Albert Einstein College of Medicine
Department Genetics
Lab Price 314
Street address 1301 Morris Park Avenue
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (10)
GSM1548727 Control_A
GSM1548728 Control_B
GSM1548729 Control_C
This SubSeries is part of SuperSeries:
GSE63287 Kdm5b depletion in embryonic stem cells does not induce intragenic promoters or affect transcription
BioProject PRJNA267724
SRA SRP050014

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63434_RAW.tar 100.0 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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