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Status |
Public on Jul 14, 2014 |
Title |
XT_100pg_rep1 |
Sample type |
SRA |
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Source name |
XT_100pg_rep1
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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 Nextera XT on 100pg 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 |
SAMN02867388 |
SRA |
SRX611277 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1416440_XT_100pg_rep1_expression.txt.gz |
381.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data included within Sample table |
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