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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 14, 2014 |
| Title |
inhouse_low_500pg_rep2 |
| Sample type |
SRA |
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| Source name |
inhouse_low_500pg_rep2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
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| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 (low) on 500pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
All reads were aligned to the human (hg19) or mouse (mm10) genomes using STAR (Dobin et al. 2013)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq (Feb 2013).
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: RPKM gene expression values (tab-delimited text)
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| Submission date |
Jun 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rickard Sandberg |
| E-mail(s) |
Rickard.Sandberg@ki.se
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| Organization name |
Karolinska Institutet
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| Department |
Department of Cell and Molecular Biology
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| Street address |
Berzelius vag 35
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| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE58652 |
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects |
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| Relations |
| BioSample |
SAMN02867366 |
| SRA |
SRX611249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1416412_inhouse_low_500pg_rep2_expression.txt.gz |
378.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data included within Sample table |
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