|
| 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
RNA180105AD_raw_1_LY3_0h_300AZ_S11_L005
|
| 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 |
|
| Relations |
| BioSample |
SAMN08918517 |
| SRA |
SRX3927032 |
