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Status |
Public on Feb 03, 2014 |
Title |
h9ESC long 2 |
Sample type |
SRA |
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Source name |
Embryonic stem cells
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Organism |
Homo sapiens |
Characteristics |
developmental stage: Embryonic stem cells cell line: H9
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Growth protocol |
The hESC H9 was grown on MEF feeders (2 Ã 104 cells/cm2) in DMEM/F12 medium plus 20% Knockout Serum Replacement (Invitrogen, Carlsbad, CA) and bFGF (4 ng/ml, Sigma-Aldrich, St. Louis, MO).
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Extracted molecule |
polyA RNA |
Extraction protocol |
10ug hESC H9 total RNA was extracted by Tri-reagent (Ambion). The mRNA was purified from total RNA by Poly(A)Purist MAG kit (Ambion) according to manufacturerâs instruction. One ug mRNA was used to synthesize first strand cDNA with oligo-dT primer by Creator SMART cDNA library Construction Kit (Clonetech). The double strand cDNA was generated from first strand cDNA solution by PCR with primers provided in the same kit.
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
454 GS FLX |
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Description |
Oligo-dT selected, oligo-dT primered. F5AGPVJ.psl GRCh37 BLAT alignment
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Data processing |
All h9ESC 454 reads and the h1ESC 454 reads (downloaded from GEO with accession number: GSE20301) are first aligned against the human reference genome (GRCh37) using BLAT. In the BLAT alignment result, a read is discarded if it shows at least one alignment with an unmapped sequence <= 20 bases in length to the human genome. Each extracted non-co-linear alignment is composed of two topologically distinct mapping parts, with a piece of overlap or gap. Both of the non-overlapping regions of mapping parts are restricted to being longer than 50 bp in length and showing greater than or equal to 95% alignment to the reference genome. The junction site between two topologically distinct genomic loci is designated as a non-co-linear junction site. For each non-co-linear alignment, two BLAT-aligned blocks, with a non-co-linear junction site, are regarded as a non-co-linear junction region. A considered non-co-linear junction region must satisfy both of the following two rules: (1) the non-co-linear junction region must show the highest level of coverage of the corresponding read in the BLAT alignment result; and (2) since the minimal length of the BLAT alignments is 20 bases, the coverage length of (1) must be at least 20 bases longer than that of all possible co-linear-fashion alignments (if they exist) in the BLAT alignment result. After that, 8,822 non-co-linear RNA candidates are extracted, which are supported by 10,135 Roche 454 reads. The BLAT alignments with two topologically distinct mapping parts are also provided (i.e., F5AGPVJ.psl).
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Submission date |
Jul 11, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Chan-Shuo Wu |
E-mail(s) |
chanshuo@gate.sinica.edu.tw
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Organization name |
Academia Sinica
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Department |
Genomics Research Center
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Street address |
128 Academia Road, Section 2, Nankang
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City |
Taipei |
ZIP/Postal code |
115 |
Country |
Taiwan |
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Platform ID |
GPL9186 |
Series (1) |
GSE30557 |
Transcriptome sequencing to systematically detect trans-splicing in human embryonic stem cells |
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Relations |
SRA |
SRX084597 |
BioSample |
SAMN00672602 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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