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Sample GSM1463936 Query DataSets for GSM1463936
Status Public on Aug 03, 2014
Title 13F-K27Ac_ChipSeq
Sample type SRA
 
Source name Neural Progenitors
Organism Mus musculus
Characteristics chip-seq antibody: H3K27Ac
antibody catalog number: Abcam AB4729
cll type: iNPC-derived from fibroblasts-clone 13F
Growth protocol Jaenisch lab- John Cassady
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against 13F-K27Ac
04252013_D24CWACXX_3.CAGATC
Data processing Images analysis and base calling was done using the solexa pipeline.
For samples MEF_WCE_ChipSeq, MEF_K27Ac_ChipSeq, 13F_WCE_ChipSeq, Sox2GFP_WCE_ChipSeq, 13F-K27Ac_ChipSeq, and Sox2GFP_K27Ac_ChipSeq reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
For samples AD-12-Med1-Skeletal_ChipSeq and AD-1-WCE-astrocytes_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 (human); mm8 (mouse)
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
 
Submission date Aug 01, 2014
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL13112
Series (1)
GSE60026 ChIP-seq of enhancer-associated transcription factors and histone modifications
Relations
BioSample SAMN02950416
SRA SRX668240

Supplementary file Size Download File type/resource
GSM1463936_04252013_D24CWACXX_3.CAGATC.wig.gz 2.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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