 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 08, 2014 |
| Title |
HEK293 GMUCT A |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293 cells
method: GMUCT
molecule: uncapped/cleaved RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy Mini Kit
TruSeq Small RNA Sample Prep Kit
GMUCT 2.0
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GMUCT
|
| 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)
|
| |
|
| Submission date |
May 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Nathan Daniel Berkowitz |
| E-mail(s) |
nberk@mail.med.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Biology
|
| Lab |
Gregory
|
| Street address |
433 S University Ave.
|
| City |
Philadelphia, |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE47121 |
Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0 |
|
| Relations |
| BioSample |
SAMN02147291 |
| SRA |
SRX283761 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1145329_HEK293_8637_counts.txt.gz |
111.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
