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| Status |
Public on Mar 08, 2014 |
| Title |
Col-0 mRNA-Seq B |
| Sample type |
SRA |
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| Source name |
flower bud
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| Organism |
Arabidopsis thaliana |
| Characteristics |
cell type: flower bud
ecotype/cultivar: Col-0
method: poly-T capture
molecule: mRNA
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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 |
poly-T capture
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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
|
| Department |
Biology
|
| Lab |
Gregory
|
| 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 |
GPL13222 |
| Series (1) |
| GSE47121 |
Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0 |
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| Relations |
| BioSample |
SAMN02147265 |
| SRA |
SRX283768 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1145336_Col0.B.txt.gz |
135.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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