GSM2630675: JQ2; Homo sapiens; RNA-Seq - SRA

SRX2832115: GSM2630675: JQ2; Homo sapiens; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 48.2M spots, 3.6G bases, 1.3Gb downloads

Submitted by: NCBI (GEO)

Study: Human basal-like breast cancer cell line HCC1143 treated with BET inhibitor JQ1 in combination with MEK inhibitor Trametinib or PI3K/mTOR inhibitor BEZ235

PRJNA323723 • SRP075882 • All experiments • All runs

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The goal of this experiment was to understand the changes in gene expression in the human basal-like breast cancer cell line HCC1143 following treatment with the MEK inhibitor Trametinib (T), PI3K/mTOR inhibitor BEZ235 (B), the BET inhibition JQ1 (JQ), Trametinib + JQ1 (TJ), or BEZ235 + JQ1(BJ), compared to a DMSO control (D). Samples were treated for 72hr and run in triplicate. Overall design: The human basal-like breast cancer cell line HCC1143 was treated for 72hr with 1uM Trametinib (T), 1uM BEZ235, 1uM JQ1 (JQ), 1uM Trametinib + 1uM JQ1 (TJ), 1uM BEZ235 + 1uM JQ1 (BJ), or a 0.05% DMSO control. Total RNA was isolated using a QIAGEN total RNA RNeasy kit, libraries were generated with a Truseq kit, and samples were run on the Nextseq500, data processing is described below.

Sample: JQ2

SAMN07138550 • SRS2207058 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: NextSeq 500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Construction protocol: Total RNA was isolated using the QIAGEN Rneasy mini kit according to manufacturers protocol Libraries were made with the Illumina Truseq Samples Prep v2 kit with 150ng RNA using manufacturer's protocol. Poly A capture: total RNA was run on the Bioanalyzer (Agilent) to verify intactness. Following this test, RNA-seq libraries were constructed using the TruSeq RNA sample prep protocol (Illumina). Poly(A)+ RNA was isolated using oligo-dT bound to magnetic beads. Poly(A)+ RNA was then chemically fragmented. RNA fragments were converted to double stranded cDNA using random hexamer priming. Fragment ends were treated to remove overhanging nucleotides and then a single “A” was added to the 3’ end of each strand to facilitate ligation. Illumina adaptors with barcode sequences was ligated to the fragments. The resulting libraries were then amplified using polymerase chain reaction with a limited number of rounds. Unincorporated nucleotides and adaptor dimers were removed using AMPure XP beads (Agencourt). Libraries were combined for multiplexing and sequenced on the NextSeq 500

Experiment attributes:

GEO Accession: GSM2630675

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 48.2M spots, 3.6G bases, 1.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR5573779	48,216,804	3.6G	1.3Gb	2017-05-30

ID:: 4068271

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Sequence Read Archive

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