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SRX1689723: GSM2113404: siProxSC_I.bam; Homo sapiens; RNA-Seq
1 ION_TORRENT (Ion Torrent Proton) run: 12.9M spots, 1.5G bases, 750.7Mb downloads

Submitted by: NCBI (GEO)
Study: Prox1 (Prosper-related homeobox 1) transcription factor depletion effect on CGTH-W-1 cells.
show Abstracthide Abstract
Analysis of CGTH-W-1 follicular thyroid carcinoma cells transcriptome following 48 hrs siRNA-mediated depletion of PROX1. PROX1 is a homeobox transcription factor. PROX1 depletion decreases migratory ability, motility and invasivness and induces profound cytoskeleton changes of CGTH-W-1 cells. Results provide insight into the role of PROX1 in the thyroid cancer. Overall design: Three biological replicates for a given condition
Sample: siProxSC_I.bam
SAMN04632357 • SRS1384143 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Ion Torrent Proton
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: RNA was isolated with GeneMATRIX Universal RNA Purification Kit, (cat. no. E3598, EURx), and RNA integrity was assessed using Agilent RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer. All transfections were performed in three independent replicates, numbered I, II and III. Efficacy of PROX1 knockdown was measured with RT-qPCR using specific primers (forward 5'-CCAGCTCCAATATGCTGAAGACCTA-3'; reverse 5'-CATCGTTGATGGCTTGACGTG-3') and Sybr Green chemistry. RNA was subjected to library preparation using Ion AmpliSeq Transcriptome Human Gene Expression Panel, according to manufacturer's protocol. Briefly, RNA was reverse transcribed and cDNA subjected to multiplex PCR reaction to amplify parts of targeted transcripts. Amplicons were then partially digested at primer sequences followed by adapters ligation to amplicons and purification on AMPure® XP beads. Resulting library was quantified on Bioanalyzer 2100 and diluted to ~100 pM prior to template preparation. Up to eight barcoded libraries were subjected to automated template preparation with Ion PI IC 200 Kit on the Ion Chef Instrument, which performs emulsion PCR on Ion Sphere particles (ISPs), followed by ISPs recovery and template loading on a PI chip. Barcoded RNA-Seq libraries samples were sequenced on a PI chip using the sequencing reagents provided as part of the Ion PI IC 200 Kit, according to the manufacturer’s instructions.
Experiment attributes:
GEO Accession: GSM2113404
Links:
Runs: 1 run, 12.9M spots, 1.5G bases, 750.7Mb
Run# of Spots# of BasesSizePublished
SRR335581812,939,5091.5G750.7Mb2016-08-01

ID:
2424499

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