GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE47164 Query DataSets for GSE47164
Status Public on Jun 08, 2015
Title Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report the chromatin binding sites of HOXB7 transcription factor in BT-474 breast cancer cell line using ChIP-sequencing. We validated the chromatin binding sites in BT-474, MDA-MB-361, MCF7 and T-47D breast cancer cell lines using ChIP-qPCR. The ChIP experiments have been performed using HOXB7 antibody and IgG non-specific antibody as a negative control. The direct downstream target genes of HOXB7 were identified by analyzing the expression of genes located nearby HOXB7 binding sites in HOXB7 knockdown versus control cells using qRT-PCR.
Overall design Examination of chromatin binding sites of HOXB7 in BT-474 breast cancer cell line using ChIP-seq. Four parallel IgG samples were sequenced, merged together and used as a control data set. Two parallel HOXB7 ChIP samples were sequenced and merged for each replicate, AF1 and AF2. Both HOXB7 ChIP replicates (AF1 and AF2) contained approximately the same amount of reads as the merged IgG control data set.
Contributor(s) Heinonen H, Lepikhova T, Sahu B, Pehkonen H, Pihlajamaa P, Louhimo R, Gao P, Wei G, Hautaniemi S, Jänne OA, Monni O
Citation(s) 26014856
Submission date May 21, 2013
Last update date Oct 08, 2019
Contact name Henna Heinonen
Organization name University of Helsinki
Street address PO Box 63
City University of Helsinki
ZIP/Postal code 00014
Country Finland
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (8)
GSM1145931 HOXB7_AF1a
GSM1145932 HOXB7_AF1b
GSM1145933 HOXB7_AF2a
BioProject PRJNA204940
SRA SRP022961

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE47164_AF1_HOXB7_MACS_peaks.bed.gz 77.4 Kb (ftp)(http) BED
GSE47164_AF2_HOXB7_MACS_peaks.bed.gz 52.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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