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| Status |
Public on Oct 04, 2012 |
| Title |
H3K4me3-A |
| Sample type |
SRA |
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| Source name |
Human primary adult proerythroblasts (ProEs)
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| Organism |
Homo sapiens |
| Characteristics |
tissue: CD34+ HSPC-derived proerythroblasts
developmental stage: adult bone marrow
chip antibody: H3K4me3
vendor: Millipore
catalog#: 04-745
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| Growth protocol |
Primary maturing fetal or adult erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq analysis using the HeliScope™ Single Molecule Sequencer, ChIP DNA was processed for 3’ polyA tailing followed by 3’ ddATP-blocking. Processing samples by ligation, amplification and size selection are not required by Helicos sequencing. Briefly, 6-9 ng of ChIP DNA or input DNA was used in the 3’ polyA tailing reaction in 14.8 ul containing 2 ul of 2.5 mM CoCl2, 2 ul of 10 x terminal transferase buffer and nuclease-free water. The reaction mixture was denatured in 95C for 5 min, followed by rapid cooling in ice water slurry. Then 1 U of terminal transferase, 4 ul of 50 uM dATP and 0.2 ul of NEB BSA were added to the mixture. Samples were incubated in a thermocycler at 37C for 1 h, 70C 10 min, followed by denaturing at 95C for 5 min and rapid cooling in ice water slurry. For 3’ ddATP-blocking, 0.5 ul of 200 uM ddATP, 1 ul of 10 x terminal transferase, 1 ul of 2.5 mM CoCl2, 1 U of terminal transferase, and 6.5 ul of nuclear-free water were added to the above reaction. Samples were incubated in a thermocycler at 37C for 1 h and 70C for 20 min. Then 2 picomoles of carrier oligonucleotide were added to the reaction, and samples were hybridized to the Helicos flow cells.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Helicos HeliScope |
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| Data processing |
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Helisphere software. Only the reads that were uniquely aligned to reference genome with read alignment score higher than 4.5 were retained for further analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file
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| Submission date |
Apr 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
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| Phone |
9015955208
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Pathology
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| Street address |
262 Danny Thomas Place, MS 345
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL14761 |
| Series (2) |
| GSE36985 |
Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis |
| GSE36994 |
Comparative profiling of human fetal and adult erythropoiesis |
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| Relations |
| Reanalyzed by |
GSE59801 |
| SRA |
SRX135015 |
| BioSample |
SAMN00848637 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM908039_H3K4me3-A.bed.gz |
102.9 Mb |
(ftp)(http) |
BED |
| GSM908039_H3K4me3-A.wig.gz |
7.4 Mb |
(ftp)(http) |
WIG |
| GSM908039_H3K4me3-A_peaks.bed.gz |
292.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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