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Sample GSM3693009 Query DataSets for GSM3693009
Status Public on Apr 30, 2019
Title A2780_pLVX_2_PAR-CLIP
Sample type SRA
Source name ovarian cancer cell line
Organism Homo sapiens
Characteristics cell line: A2780
genotype: empty lentivirus vector
cell type: ovarian cancer
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
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.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 3000
Description RNA bound to AGO
replicate 2
Data processing Library strategy: PAR-CLIP
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
Submission date Mar 29, 2019
Last update date May 01, 2019
Contact name Markus Hafner
Organization name NIH
Department NIAMS
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL21290
Series (1)
GSE129076 miR-450a acts as a tumor suppressor in ovarian cancer by readjusting energy metabolism
BioSample SAMN11289303
SRA SRX5604727

Supplementary file Size Download File type/resource
GSM3693009_A2780_pLVX_PAR-CLIP_replicate_2.xlsx 2.3 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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