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| Status |
Public on Apr 01, 2022 |
| Title |
PC3_pGIPZ_HOXB13 |
| Sample type |
SRA |
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| Source name |
prostate tumor
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| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
treatment: pGIPZ
antibody: HOXB13, Santa Cruz, sc-66923, F0710
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| Treatment protocol |
LNCaP cells were infected with control shRNA (pGIPZ), shRNA targeting HOXB13 (shHOXB13), shHOXB13 with concomitant infection by HOXB13-WT or G84E lentiviruses for 7 days.
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| Growth protocol |
LNCaP and PC3 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antibody. DNA was then reverse crosslinked from protein and purified. ChIP-seq libraries were prepared from 3-5ng ChIPped DNA by using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
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| Description |
PC3_pGIPZ_HOXB13
m681
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| Data processing |
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file
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| Submission date |
Feb 07, 2021 |
| Last update date |
Apr 01, 2022 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan.yu@emory.edu
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| Organization name |
Emory University
|
| Department |
Urology
|
| Lab |
Jindan Yu's lab
|
| Street address |
E330, 1760 Haygood Dr NE
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL15456 |
| Series (2) |
| GSE153583 |
HOXB13 inhibits lipid metabolism through HDAC3-mediated epigenetic reprogramming [ChIP-Seq] |
| GSE153586 |
HOXB13 inhibits lipid metabolism through HDAC3-mediated epigenetic reprogramming |
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| Relations |
| BioSample |
SAMN17825644 |
| SRA |
SRX10045323 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5068231_m681.bedgraph.gz |
49.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM5068231_m681_peak.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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