|
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |