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| Status |
Public on Feb 25, 2017 |
| Title |
r_IbSP |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Mantle cell lymphoma cells
source: bone marrow
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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)
Supplementary_files_format_and_content: .xls RPKM values
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| Submission date |
Feb 26, 2014 |
| 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) |
| GSE55405 |
Cell Cycle Reprogramming for PI3K Inhibition Overrides Relapse-Specific C481S BTK Mutation Revealed by Longitudinal Functional Genomics in Mantle Cell Lymphoma |
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| Relations |
| BioSample |
SAMN02665818 |
| SRA |
SRX476486 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1335489_r_IbSP.xls.gz |
1.4 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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