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Status |
Public on Mar 08, 2014 |
Title |
K562 GMUCT B |
Sample type |
SRA |
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Source name |
K562 cells
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Organism |
Homo sapiens |
Characteristics |
cell type: K562 cells method: GMUCT molecule: uncapped/cleaved RNA
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Extracted molecule |
total RNA |
Extraction protocol |
miRNeasy Mini Kit TruSeq Small RNA Sample Prep Kit GMUCT 2.0
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2000 |
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Description |
GMUCT
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Data processing |
Basecalls performed with most up-to-date version of Illumina base calling software 3' adapter sequences were trimmed using cutadapt (version 0.9.5 with parameters -e 0.06 -O 6 -m 14), and reads were subsequently aligned to the genome using bowtie (human) or tophat (Arabidopsis) read counts per transcript were found using HTSeq Genome_build: hg19 (Arabidopsis) or TAIR9 (human cell line)
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Submission date |
May 20, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Nathan Daniel Berkowitz |
E-mail(s) |
nberk@mail.med.upenn.edu
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Organization name |
University of Pennsylvania
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Department |
Biology
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Lab |
Gregory
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Street address |
433 S University Ave.
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City |
Philadelphia, |
State/province |
Pennsylvania |
ZIP/Postal code |
19104 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE47121 |
Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0 |
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Relations |
BioSample |
SAMN02147261 |
SRA |
SRX283766 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1145334_K562_8642_counts.txt.gz |
109.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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