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| Status |
Public on Jul 11, 2016 |
| Title |
siHOXC11 rep1 |
| Sample type |
SRA |
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| Source name |
LY2 cells
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| Organism |
Homo sapiens |
| Characteristics |
origin: breast epithelial
sirna: siRNA-HOXC11
cell line: MCF7-derived LY2
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| Treatment protocol |
LY2 cells were seeded at a density of 2.5x10e5 and incubated overnight under standard conditions. HOXC11 was silenced by transient transfection using an experimentally verified pool of siRNA (Flexitube, Qiagen, UK) (2μg siRNA/6well) . All transfections were carried out using Lipofectamine 2000 transfection reagent according to manufacturer’s instructions (Invitrogen, UK) and a non-targeting siRNA negative control (Ambion, UK) was used as a control for all siRNA experiments. Both siRNA and scambled controls were treated with tamoxifen (10-8M) (24 hours) before cells were pelleted and RNA extracted,
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| Growth protocol |
MCF7-derived LY2 (Bronzert et al., 1985) were maintained in phenol red-free Eagle’s minimum essential medium with 2 mM L-glutamine and supplemented with charcoal dextran stripped fetal bovine serum, 10% (Invitrogen, Paisley, UK).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using an RNeasy (Qiagen, UK) according to manufacturer's instractions.
Libraries were perepared according to standard Illumina protocols. Four independent biological libraries were prepared for each sample to facilitate the expression detection and variance estimation. Multiplexing was achieved using in-house designed barcoding adapters Four biological replicates of either siHOXC11 or scrHOXC11 sample were sequenced on a flow cell. Two replicates, one from each sample, were multiplexed and loaded on a single lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
s_1_si3
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| Data processing |
de-multiplex of raw data was performed using customized scripts
short reads were mapped to the reference genome using tophat program version 1.2.0
Not all the raw data passed our initial QC. Only samples s_1_scr2 (scrHOXC11 rep1), s_2_scr3 (scrHOXC11 rep2), s_1_si3 (siHOXC11 rep1) & s_2_si2 (siHOXC11 rep2) passed and were used for further analysis.
differential expression test was performed using cutfflink/cuffdiff program version 1.0.2
Genome_build: Ensembl GRCh37 release 64 (hg19)
Supplementary_files_format_and_content: differential expression targets from cuffdiff output, including gene ids, locus, FPKM, fold changes, p-values.
The processed file is the output results from CuffDiff. The fields "value_1" and "value_2" correspond to an average FPKM expression of two samples (Value_1 = ave. s_1_scr2 & s_2_scr3; Value_2 = ave. s_1_si3 & s_2_si2).
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| Submission date |
Jul 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Leonie Young |
| Organization name |
Royal College of Surgeons, Ireland
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| Department |
Surgery
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| Lab |
Endocrine Oncology Research Group
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| Street address |
York Street
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| City |
Dublin |
| ZIP/Postal code |
Dublin 2 |
| Country |
Ireland |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE71139 |
RNA-sequencing of tamoxifen resistant LY2 cells transfected with siRNA-HOXC11. |
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| Relations |
| BioSample |
SAMN03893540 |
| SRA |
SRX1115978 |
| 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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