|
| Status |
Public on Apr 28, 2011 |
| Title |
THP1_hCAGE_low_quantity_1000ng_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
starting total rna: 1000ng
cell line: THP-1
|
| Growth protocol |
THP-1 cells were cultured in RPMI1640 (Invitrogen) supplemented with 10% FBS, Penicillin/Streptomycin (Invitrogen), 10 mM HEPES (Invitrogen), 1 mM sodium pyruvate and 50 µM 2-mercaptoethanol. HeLa cells were cultured in Eagleâs MEM (Invitrogen) supplemented with 10% FBS, 1% NEAA (Invitrogen) and Penicillin/Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
First strand cDNA is generated from total RNA using an excess of random primer. 5’ end complete first strand cDNAs are captured for capped RNAs. First strand cDNA is polyA tailed and blocked and then loaded directly onto the HeliScope flow cell for sequencing. MPG beads are used in cap-trapping step for the standard protocol (for starting from 5ug or more total RNA), and DYNAL M270 streptavidin magnetic beads (Life Technologies) are used for low quantity version (less than 1ug). Further details are written in the manuscript.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
THP1.LqDynal.1000ng.2nd_20100527.Riken4.fc1.ch5
|
| Data processing |
After the filtering with filterSMS in HeliSphere package, the obtained reads are aligned to the human genome (hg18) with indexDPgenomic and only the alignments with the best alignment score in unique location are selected. Gene expression counts (Matrix hCAGE_non-normalized) represent calcurated from the read counts in the +/- 500bp region from RefSeq. The expression counts are normalized as tpm (tags per million), where expression counts are divided by the total number of mapped reads and multiplied by one million (hCAGE_normalized.txt).
|
| |
|
| Submission date |
Mar 24, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Hideya Kawaji |
| E-mail(s) |
kawaji@gsc.riken.jp
|
| Organization name |
RIKEN
|
| Department |
Omics Science Center
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14761 |
| Series (1) |
| GSE28148 |
Unamplified Cap Analysis of Gene Expression on a single molecule sequencer (HeliScopeCAGE) |
|
| Relations |
| SRA |
DRX000599 |
| BioSample |
SAMN02198645 |
