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Sample GSM651559 Query DataSets for GSM651559
Status Public on Jul 01, 2011
Title CD34_Nucleosome
Sample type SRA
 
Source name CD34
Organism Homo sapiens
Characteristics condition: CD34 WT
Treatment protocol As described in (Cui et al. Cell Stem Cell. 2009 (PMID: 19128795)
Growth protocol As described in (Cui et al. Cell Stem Cell. 2009 (PMID: 19128795)
Extracted molecule genomic DNA
Extraction protocol X-linked CD34 or CD36 cells were sonicated to about 200-500 bp of the DNA fragment to prepare the chromatin templates. Four or eight microgram of antibodies were used to incubate with chromatin templates. The resulting ChIP-DNA was used for library construction according to the protocol (Cui et al. Cell Stem Cell. 2009 (PMID: 19128795)). Basically, DNA was end-repaired and ligated with adapters Ligation products wer amplified with 17 cycles and purified from agrose gel. DNA concentration was measured before the loading to machine.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description MNase-Seq following crosslink & Mnase
Data processing Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline (Eland). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries). The ChIP-enriched peaks were identified by MACS for CTCF, GATA1 and TAL1 (PMID: 18798982) and by SICER for BRG1 (PMID: 19505939). Nucleosome tag enriched regions were identified by the NPS package (PMID: 19014516).
 
Submission date Jan 07, 2011
Last update date May 15, 2019
Contact name Gangqing Hu
E-mail(s) michael.hu@hsc.wvu.edu
Organization name West Virginia University
Department MicroBiology, Immunology, and Cell Biology
Lab 2072A, HSC North, Floor 2
Street address 64 Medical Center Drive
City Morgantown
State/province West Virginia
ZIP/Postal code 26506-9177
Country USA
 
Platform ID GPL9052
Series (1)
GSE26501 Regulation of nucleosome landscape and transcription factor binding at enhancers by BRG1
Relations
SRA SRX037953
BioSample SAMN00190808

Supplementary file Size Download File type/resource
GSM651559_GA1511_human_CD34_Nuc_r401_l7_noDup.bed.gz 47.9 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r403_l1_noDup.bed.gz 42.8 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r406_l7_noDup.bed.gz 48.8 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r408_l1_noDup.bed.gz 41.9 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r408_l2_noDup.bed.gz 40.3 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r408_l3_noDup.bed.gz 41.9 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r408_l4_noDup.bed.gz 43.3 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r408_l5_noDup.bed.gz 43.8 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r408_l6_noDup.bed.gz 45.6 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r408_l7_noDup.bed.gz 46.6 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r409_l2_noDup.bed.gz 45.6 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r409_l3_noDup.bed.gz 47.1 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r409_l4_noDup.bed.gz 47.0 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r409_l5_noDup.bed.gz 48.3 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r409_l6_noDup.bed.gz 49.8 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r409_l7_noDup.bed.gz 50.0 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r410_l1_noDup.bed.gz 46.3 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r410_l2_noDup.bed.gz 45.2 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r410_l3_noDup.bed.gz 45.1 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r410_l4_noDup.bed.gz 45.9 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r410_l5_noDup.bed.gz 46.6 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r410_l6_noDup.bed.gz 46.5 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r410_l7_noDup.bed.gz 46.5 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r411_l5_noDup.bed.gz 55.4 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r411_l6_noDup.bed.gz 55.7 Mb (ftp)(http) BED
GSM651559_GA1511_human_CD34_Nuc_r411_l7_noDup.bed.gz 56.4 Mb (ftp)(http) BED
GSM651559_cd34_nucs_NPS.txt.gz 57.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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