GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM830121 Query DataSets for GSM830121
Status Public on Jun 18, 2012
Title p63 Progenitor
Sample type SRA
Source name keratinocytes
Organism Homo sapiens
Characteristics chip antibody: anti-p63 4A4
chip antibody vendor: Santa Cruz
chip antibody lot#: n/a
chip antibody catalog#: n/a
cell type: neonatal keratinocytes
differentiation stage: progenitor
Growth protocol Keratinocytes were grown in Gibco SFM medium till 100% confluent with addition of 1.2 mM Ca2+ for 3 Days to induce differentiation.
Extracted molecule genomic DNA
Extraction protocol Cells are crosslinked in 1% formaldehyde and lysates clarified by sonication. p63 DNA comlplexes were isolated using Santa Cruz anti-p63 4A4 antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Description p63 ChIP
Data processing Reads in each samples were aligned using "Bowtie"(version 0.12.6). Peaking calling was performed by "MACS" (version 1.4.0rc2). For complete methods please refer to the paper.
Submission date Nov 09, 2011
Last update date Oct 11, 2022
Contact name Douglas Porter
Organization name Stanford
Department Dermatology
Lab Khavari
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL9115
Series (2)
GSE33571 Disrupted transcriptional network in ΔNp63 AEC tissue model [ChIP-Seq]
GSE33572 Disrupted transcripitonal network in ΔNp63 AEC tissue model
SRA SRX105186
BioSample SAMN00752406

Supplementary file Size Download File type/resource 41.7 Mb (ftp)(http) BW
GSM830121_d0_p63.sam.gz 645.3 Mb (ftp)(http) SAM
GSM830121_d0_p63_peaks.bed.gz 57.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap