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Sample GSM1689150 Query DataSets for GSM1689150
Status Public on May 28, 2015
Title Jurkat_polyA_RNA-Seq
Sample type SRA
Source name T-ALL
Organism Homo sapiens
Characteristics cell type: Jurkat
Growth protocol Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 10 min.
Extracted molecule polyA RNA
Extraction protocol Using 10 μg of total RNA, we prepared sequencing libraries according to the following protocol. Polyadenylated RNA was purified by two rounds of selection with Dynabeads mRNA Purification Kit for mRNA Purification from total RNA (Life Technologies, 610-06) following the manufacturer instructions. This resulting RNA was then further processed for RNA-Seq assays. Briefly, polyadenylated RNA was fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase (Life Technologies, 18080-051). Second strand cDNA synthesis was performed by using RNase H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. After cDNA synthesis, the double-stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified by using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicenter, HU59100). The adaptor ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified by using gel electrophoresis. These RNA-Seq libraries were subsequently sequenced on Illumina HiSeq 2000. Sequences were aligned by using Bowtie (version 0.12.2) to build version HG19 of the human. The RPKM (reads per kilobase of exon per million) was then computed for each gene.
Total RNA was purified using mirVana miRNA isolation kit (Life technologies) following the manufacturer instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Aligned using TopHat v2.0.13 with configuration: library-type fr-firststrand -p 40 --microexon-search --coverage-search
Supplementary_files_format_and_content: Aligned reads were first separated into strand/direction using samtools view. Density of strand-separated reads in 50bp bins was calculated using genomeCoverageBed. The union of the resulting bedGraph files was taken using unionBedGraphs and converted to WIG format using (
Submission date May 18, 2015
Last update date May 15, 2019
Contact name Richard A Young
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platform ID GPL11154
Series (2)
GSE68975 Activation of proto-oncogenes by disruption of chromosome neighborhoods [RNA-Seq]
GSE68978 Activation of proto-oncogenes by disruption of chromosome neighborhoods
BioSample SAMN03700050
SRA SRX1030322
Named Annotation GSM1689150_Jurkat_RNASeq_hg19_pos.wig.gz
Named Annotation GSM1689150_Jurkat_RNASeq_hg19_neg.wig.gz

Supplementary file Size Download File type/resource
GSM1689150_Jurkat_RNASeq_hg19_neg.wig.gz 5.8 Mb (ftp)(http) WIG
GSM1689150_Jurkat_RNASeq_hg19_pos.wig.gz 5.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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