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Sample GSM908054 Query DataSets for GSM908054
Status Public on Oct 04, 2012
Title TAL1-F
Sample type SRA
 
Source name Human primary fetal proerythroblasts (ProEs)
Organism Homo sapiens
Characteristics tissue: CD34+ HSPC-derived proerythroblasts
developmental stage: 2-trimester fetal liver
chip antibody: TAL1
vendor: Santa Cruz Biotechnology
catalog#: sc-12984
Growth protocol Primary maturing fetal or adult erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Helicos HeliScope
 
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
 
Submission date Apr 02, 2012
Last update date May 15, 2019
Contact name Jian Xu
E-mail(s) Jian.Xu@stjude.org
Phone 9015955208
Organization name St. Jude Children's Research Hospital
Department Pathology
Street address 262 Danny Thomas Place, MS 345
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
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
Relations
SRA SRX135030
BioSample SAMN00848652

Supplementary file Size Download File type/resource
GSM908054_TAL1-F.bed.gz 85.0 Mb (ftp)(http) BED
GSM908054_TAL1-F.wig.gz 12.0 Mb (ftp)(http) WIG
GSM908054_TAL1-F_peaks.bed.gz 83.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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