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| Status |
Public on Mar 07, 2012 |
| Title |
NCCIT_mRNA_seq |
| Sample type |
SRA |
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| Source name |
NCCIT, mRNA
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT
cell type: embryonic carcinoma cells
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| Growth protocol |
NCCIT embryonic carcinoma cell lines on a 10cm dish were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% antibiotic-antimycotic solution (Hyclone) at 37ºC in a humidified atmosphere composed of 5% CO2.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction and preparation: The sequencing library of mRNA was generated by using the mRNA-seq sample prep kit (Illumina, San Diego, CA). Polyadenylated mRNA was purified from 10g of total RNA by Sera-mag oligo(dT) beads (Illumina). The mRNA was fragmented by incubating with fragmentation buffer (Illumina) at 94oC for 5 min. First strand cDNA was synthesized by SuperScript II (Invitrogen) and random primers (Illumina). Second strand cDNA was synthesized by RNaseH and DNA ol I (Illumina). cDNA fragments were ligated to a pair of adaptors for sequencing on the Illumina Genome Analyzer. The ligation products were size-fractioned to obtain 200 bp fragments on a 2% agarose gel and subjected to 15 cycles of PCR amplification. Cluster generation and 72 cycles of single-read sequencing were done.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
polyA RNA
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| Data processing |
For mRNA-seq, the sequence tags were mapped to the human genome (UCSC hg18) by using TopHat40 with default parameters. The mapped sequence reads were extended to the average size of fragment length (200bp).
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| Submission date |
Dec 21, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Inkyung Jung |
| E-mail(s) |
ijungkaist@gmail.com
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| Organization name |
KAIST
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| Department |
Biological Sciences
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| Street address |
KAIST, 291 Daehak-ro, Yuseong-gu
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE25882 |
Genome-wide maps of chromatin state in NCCIT cells |
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| Relations |
| SRA |
SRX037079 |
| BioSample |
SAMN00189378 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM644996_tophat_result_mRNAseq.sam.gz |
1.7 Gb |
(ftp)(http) |
SAM |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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