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| Status |
Public on Apr 30, 2019 |
| Title |
A2780_450B_2_small_RNA-Seq |
| Sample type |
SRA |
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| Source name |
ovarian cancer cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A2780
genotype: pri-miR-450b overexpression with lentivirus
cell type: ovarian cancer
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| Growth protocol |
A2780 and SKOV-3 were cultivated either in RPMI medium (Gibco, Catalog No. 31800–022) or in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, Catalog No. 11995065), respectively, supplemented with 10% fetal bovine serum (FBS, GE Healthcare, Catalog No. SH30071.03) and 100 units of penicillin and 0,1 mg/ ml of streptomycin (Sigma-Aldrich Co., Catalog No. P4333). Cells were cultivated at 37°C and 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from three biological replicates from each cell line using TRIzol™ Reagent (Invitrogen, Catalog No. 15596026) second to recommendations from manufacturer. For small RNA cDNA library, we followed the protocol from Farazi et al (Farazi et al., 2012) after RNA extraction. AGO 4SU-PAR-CLIP method was performed as described previously (Benhalevy et al., 2016; Hafner et al., 2010)
All the samples were sequenced on an Illumina HiSeq 3000 machine using the 50 cycle single read protocol.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
small RNA
replicate 2
A2780_mature_miRNAs_relative_freq.xlsx A2780_prec_miRNAs_relative_freq.xlsx
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| Data processing |
For RNA-Seq and small RNA-Seq, the sequence reads were aligned to the human genome h19 using TopHat.Differential expression was performed using Cuffdiff
For AGO 4SU-PAR-CLIP, the analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Genome_build: h19
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| Submission date |
Mar 29, 2019 |
| Last update date |
Apr 30, 2019 |
| Contact name |
Markus Hafner |
| E-mail(s) |
markus.hafner@nih.gov
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| Organization name |
NIH
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| Department |
NIAMS
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| Street address |
50 South Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE129076 |
miR-450a acts as a tumor suppressor in ovarian cancer by readjusting energy metabolism |
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| Relations |
| BioSample |
SAMN11289307 |
| SRA |
SRX5604724 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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