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| Status |
Public on Mar 11, 2015 |
| Title |
Ad-NERKI, Vehicle, rep 3 |
| Sample type |
SRA |
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| Source name |
hFOB 1.19 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: osteoblastic cell
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| Treatment protocol |
hFOB cells were plated in 10-cm culture dishes (n=6) at a final density of 2 × 10^4 cells/cm2. Cells were infected at the time of plating at a multiplicity of infection (MOI) of 15 (Ad-ERα), 30 (Ad-NERKI) and 22.5 (Ad-NOER). Following another 24 hour incubation to allow for complete infection, the cells were treated with either ethanol vehicle (0.1% v/v) or 10 nM 17-β-estradiol (0.1% v/v; Sigma-Aldrich) in the presence of media containing triple-stripped charcoal-treated FBS for an additional 24 hrs.
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| Growth protocol |
The hFOB 1.19 human fetal osteoblastic cell line (hFOB) was passaged in phenol red-free αMEM growth medium (Invitrogen, Carlsbad, CA) supplemented with 1X antibiotic/antimycotic (Invitrogen), 10% (v/v) fetal bovine serum (Hyclone, Logan, UT) and 300 ug/mL G418 selection antibiotic.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using RNeasy minicolumns (Qiagen, Valencia, CA) and treated with RNase-free DNase (Qiagen) to remove potential contaminating DNA.
RNA libraries for RNAseq analysis were prepared from 100 ng of isolated total RNA from each sample using the manufacturer’s instructions. Unique indexes were incorporated at the adaptor ligation step for loading multiple samples per flow cell. Three distinct indexed libraries were loaded per flow cell and sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8). Base calling was performed using Illumina RTA (version 1.12.4.2). An average of 130 million reads per sample was achieved resulting in ~96% mapped reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and count values for each Sample
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| Submission date |
Mar 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
David George Monroe |
| E-mail(s) |
Monroe.David@mayo.edu
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| Phone |
507-538-6517
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| Organization name |
Mayo Clinic
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| Department |
Endocrinology
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| Street address |
200 1st St SW
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE55769 |
Dissection of estrogen receptor alpha signaling pathways in osteoblasts using RNA-sequencing |
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| Relations |
| BioSample |
SAMN02687559 |
| SRA |
SRX484192 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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