GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM364526 Query DataSets for GSM364526
Status Public on Sep 08, 2009
Title Illumina sequenced synthetic miRNA sample A with barcode 2
Sample type SRA
Source name Sample A
Organism Homo sapiens
Characteristics sample: synthetic miRNA
Biomaterial provider Integrated DNA Technologies
Treatment protocol n/a
Growth protocol n/a
Extracted molecule other
Extraction protocol n/a
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina Genome Analyzer
Description Illumina barcode 2 (CGGA)
Illumina multiplexed sequencing
Data processing The GAPipeline-1.0 was used starting from the IPAR-1.01 calculated intensities.
The adapter sequences were trimmed in 3 steps:
(NB: 3' special adapter: CTGTAGGCACCATCAATCGTA)
1) The 21nt adapter sequence is used, which permits to identify “inserts” of 11nt or less.
2) If no adapter sequence was found, in successive steps the last base of the adapter was removed and the sequence was searched at the end of the reads. The minimum adapter size of 6 bases permits identifying inserts of up to 26 bases.
3) Finally the remaining reads are search for notexact matches of the adapter. The first 5 bases of the adapter were searched within the full reads sequences and at least 80% of the following bases must be identical to the adapter sequence (max 26 bp).
Submission date Jan 26, 2009
Last update date Jun 11, 2013
Contact name Hanni Willenbrock
Phone +45 45 66 09 85
Organization name DTU
Department Center for Biological Sequence Analysis
Street address Kemikalievej, bygning 208
City Kgs. Lyngby
ZIP/Postal code 2800
Country Denmark
Platform ID GPL9052
Series (1)
GSE14511 Quantification of synthetic miRNAs
BioSample SAMN02195511

Data table header descriptions
Concentration concentration of the sequence in amol/ul
COUNT number of times sequenced

Data table
SEQUENCE Concentration COUNT
hsa-let-7e* 376.470588235294 350
hsa-let-7g 376.470588235294 926
hsa-miR-125a-5p 376.470588235294 1099
hsa-miR-139-5p 376.470588235294 111
hsa-miR-181d 376.470588235294 3235
hsa-miR-182* 376.470588235294 614
hsa-miR-193a-3p 376.470588235294 3
hsa-miR-197 376.470588235294 24
hsa-miR-222 376.470588235294 512
hsa-miR-24-2* 376.470588235294 23
hsa-miR-302a 376.470588235294 5329
hsa-miR-30e 376.470588235294 1500
hsa-miR-335* 376.470588235294 766
hsa-miR-33a 376.470588235294 31
hsa-miR-33b* 376.470588235294 31
hsa-miR-342-3p 376.470588235294 138
hsa-miR-361-5p 376.470588235294 1147
hsa-miR-432 376.470588235294 8903
hsa-miR-449b 376.470588235294 212
hsa-miR-485-5p 376.470588235294 8693

Total number of rows: 744

Table truncated, full table size 20 Kbytes.

Supplementary file Size Download File type/resource 26.6 Mb (ftp)(http) ZIP
Processed data included within Sample table
Raw data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap