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Sample GSM3094216 Query DataSets for GSM3094216
Status Public on Apr 13, 2018
Title OCI-LY3 0H_1
Sample type SRA
Source name OCI-LY3 0H
Organism Homo sapiens
Characteristics cell line: OCI-LY3
cell type: diffuse large B-cell lymphoma (DLBCL) cell line
treated with: none (untreated)
Treatment protocol Both cell lines were plated at one million cells in a 6 well plate in 2mL of the media listed above. Time 0 cells were collected at the same time as treatment (300nM of AZ5576) of the 3 and 6 hour samples.
Growth protocol Both cell lines were grown in RPMI 1640 supplemented with 10% FBS and 1% pencillin streptomycin in a T75 flasks. Both cell lines were kept in 5% CO2 and 37 celsius
Extracted molecule total RNA
Extraction protocol Both cell lines at time 0, 3 hours, or 6 hours were collected and spun in a table top centrifuge for 5 min at 800xg. They were washed with PBS and respun for 5 min at 800xg. Countertops were then sprayed with Rnase spray (Fisher cat no. 7002). Samples were homogenized with Omega Homogenizer columns and total RNA was collected with the Omega E.Z.N.A. Total RNA kit
Total RNA was run on the Bioanalyzer (Agilent) to verify intactness. Following this test, RNA-seq libraries were constructed using Illumina's TruSeq RNA Library Prep Kit v2: Poly(A)+ RNA was isolated from 200ng of total RNA using oligo-dT bound to magnetic beads. The resulting 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. Unique Illumina adaptors with barcode sequences were ligated to the fragments. The resulting libraries were then amplified using 13-rounds of PCR. Unincorporated nucleotides and adaptor dimers were removed using AMPure XP beads (Agencourt). Libraries were quantitated using qPCR (Kapa Biosystems), pooled for multiplexing, 6 samples per lane, and sequenced on a HiSeq 2500 sequencer (Illumina) on a Single Read flow cell, 100 cycles.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description RNA180105AD_1_LY3_0h
Data processing Illumina
Alignment: STAR2.5.3a, Default parameters
Filtering: Genes expressed in at least one sample
Differential Expression/Normalization: DESeq2 rld (regularlized log transform)
Genome_build: grch38
Supplementary_files_format_and_content: Tab delimited files
Submission date Apr 12, 2018
Last update date Apr 13, 2018
Contact name Alexey Danilov
Organization name Oregon Health and Science Univeristy
Street address 3181 SW Sam Jackson Pk Rd
City Portland
State/province OR
ZIP/Postal code 97219
Country USA
Platform ID GPL16791
Series (1)
GSE113035 Seletive inhibition of CDK9 in DLBCL cell lines
BioSample SAMN08918517
SRA SRX3927032

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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