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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 14, 2018 |
| Title |
Primary MCL #3 |
| Sample type |
SRA |
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| Source name |
Lymph Node
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Mantle cell lymphoma cells
source: Mantle cell lymphoma Patient
disease state: Mantle Cell Lymphoma
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| Treatment protocol |
No treatment
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| Growth protocol |
Mantle cell lymphoma (MCL) biopsies were obtained from patients at the New York-Presbyterian Hospital after informed consent as part of a study approved by the Institutional Review Board. Primary MCL cells were purified using MACS CD19 MicroBeads (Miltenyi Biotec). The percentage of MCL tumor cells (CD19+, CD5+, CD23-) was determined to be > 90% by flow cytometry. B cells from healthy volunteers were isolated from peripheral blood (PBC)s using the same protocol. Primary MCL cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FBS (HyClone), 2 mM L-glutamine and 100 U/ml penicillin/streptomycin (Invitrogen)
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| Extracted molecule |
total RNA |
| Extraction protocol |
For each experimental condition, 100 ng of high quality total RNA (RIN > 0.8 on the Agilent BioAnalyzer 2100) was isolated using the RNAEasy kit according to the manufacturer’s instructions (QIAGEN)
All RNAs were converted to cDNA, isolated with magnetic beads from the TruSeq mRNA prep kit (v2), and then ligated to Illumina adapters, as per the standard TruSeq Illumina protocol. Using these multi-plexed cDNA libraries, we generated clusters on the Illumina cBot station and paired-end sequenced each sample to 50x50 bp on the Illumina HiSeq2000 at the Weill Cornell Medical College (WCMC) Epigenomics Core
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Cluster generation, sequencing, and processing of the images were done using the Real-Time Analysis (RTA) software on the HiSeq2000 and post-processing with CASAVA (v.1.8.2).
To optimize library preparation we used a TACON high-throughput RNA prep-station. Raw data were filtered for high median quality (Q-value > 20) and then sent to Cornell’s High Performance Computing (HPC) cluster, to be run through our RNA-seq analysis pipeline.
Raw reads were trimmed for the first and last five base pairs before alignment to remove low quality bases.
Our RNA-Seq analysis pipeline used BWA and SAMtools.
Processed Data files (RPKM values) were obtained using Genesifter (Geospiza), which uses SAMtools and the Genome Analysis Toolkit (GATK) for base quality score recalibration and local re-alignment for indels.
Genome_build: Human (Build 37.2)
upplementary_files_format_and_content: .txt RPKM values
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| Submission date |
May 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Selina Chen-Kiang |
| E-mail(s) |
sckiang@med.cornell.edu
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| Organization name |
Weill Cornell Medical College
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| Street address |
1300 York Avenue, C338
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE46846 |
Induction of Prolonged Early G1 Arrest by CDK4/CDK6 Inhibition Reprograms Lymphoma Cells for Durable PI3Kδ Inhibition Through PIK3IP1 |
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| Relations |
| BioSample |
SAMN02142101 |
| SRA |
SRX277272 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1139101_Primary_MCL__3.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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