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| Status |
Public on Jan 11, 2016 |
| Title |
LY1_CON_4EIP_R2 |
| Sample type |
SRA |
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| Source name |
OCI-LY1 cells
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| Organism |
Homo sapiens |
| Characteristics |
molecule: eIF4E RIP nuclear RNAs
differential expression tool: pairwise limma voom
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| Treatment protocol |
None
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| Growth protocol |
IMDM, 10% FBS, pen/strep
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| Extracted molecule |
total RNA |
| Extraction protocol |
RIP then Trizol
Illumina TruSeq Stranded Total RNA sample prep
RIP-seq: Nuclear input samples were taken before 1 mg of nuclear lysate was used for eIF4E RIP. Complexes were eluted by boiling with Tris-EDTA containing 1% SDS and 12% beta-mercaptoethanol. RIP RNA and nuclear input RNA was isolated using Trizol (Life Technologies). mRNA-seq: RNA was isolated using Trizol (Life Technologies).
Genomic DNA was eliminate with Dnase treatment, and total RNA was taken into the Illumina TruSeq Stranded Total RNA library prekit (RIP-seq samples) or mRNA was isolated using two rounds of poly-T oligo attached magnetics beads and then taken into the Illumina TruSeq RNA sample prep kit (PDX RNAseq).
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Paired_analysis_DE.txt
LY1_4EIP_allreps_counts.txt
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Reads that passed filter were aligned to hg19 using STAR (Dobin et al., 2012).
Gene expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/ HTSeq/).
Differentially enriched genes were identified with pairwise limma analysis on voom normalized counts (RIP-seq samples). Genes with a FDR-corrected p-value < 0.05 were considered differentially expressed.
Differentially expressed genes in the PDX samples were identified with the edgeR package (Robinson et al., 2010, PDX samples). Genes with a FDR-corrected p-value < 0.05 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count and the limma analysis and edgeR outputs are provided as a .txt file.
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| Submission date |
Nov 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tharu M Fernando |
| E-mail(s) |
tmf2001@med.cornell.edu
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| Phone |
646-962-6728
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| Organization name |
Weill Cornell Medical College
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| Department |
Medicine, Heme-Onc
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| Lab |
Ari Melnick
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| Street address |
413 East 69th St BB1462
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE63265 |
Combinatorial targeting of nuclear export and translation of RNA inhibits aggressive B-cell lymphoma |
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| Relations |
| BioSample |
SAMN04244482 |
| SRA |
SRX1420993 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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