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Sample GSM1164636 Query DataSets for GSM1164636
Status Public on Dec 25, 2013
Title HSC_H3K27me3_rep2
Sample type SRA
Source name HSC in vitro expanded bone marrow cells transduced with Nup98-HoxB4
Organism Mus musculus
Characteristics cell type: in vitro expanded bone marrow cells transduced with Nup98-HoxB4
strain: B6
chip antibody: anti H3K27me3 antibody (Cell Signaling #9733)
chip antibody catalog #: #9733
chip antibody manufacturer: Cell Signaling
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to Illumina's instructions accompanying the Agilent_DNA _Kit _100. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were generated and sequenced on the Genome Analyzer following the Illumina manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Sequence reads were mapped using Botwie version 0.12.7 with up to 2 mismatches and up to 100 best alignment positions were reported (bowtie options –v 2 –a --best --strata –m 100).
In case a read had more hits n to an individual sequence from any of these data bases, the weight 1/n was used instead. These weights were used in all the subsequent analyses. DNA fragment length was estimated from cross correlation. profile of read density on both chromosomal strands.
Mapped reads were shifted towards their 3’ end by the half of the fragment length
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated with a custom Perl script
Submission date Jun 16, 2013
Last update date May 15, 2019
Contact name maria alessandra vigano
Organization name university of basel
Department department of biomedicine
Street address mattenstrasse,28
City basel
ZIP/Postal code 4058
Country Switzerland
Platform ID GPL11002
Series (1)
GSE47995 An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.
BioSample SAMN02204648
SRA SRX306589

Supplementary file Size Download File type/resource
GSM1164636_Sample5_ChIP_H3K27me3_Nup-Hox_HSC.mm9-mmV02-aln2.w100.m100.wig.gz 24.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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