|
| Status |
Public on Oct 10, 2011 |
| Title |
ECC1_Tn-RNA-seq_1pg_mRNA |
| Sample type |
SRA |
| |
|
| Source name |
ECC-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ECC-1
protocol: Tn-RNA-seq
mrna input: 1 pg
|
| Growth protocol |
The human endometrial  cancer cell line ECC-1 was grown in RPMI-1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) and 1% penicillin-streptomycin (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library construction protocols are indicated in the characteristics: Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq from poly(A) selected mRNA
|
| Data processing |
To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters: --phred64-quals -n 2 -k 1 -m 10 â-best. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.
|
| |
|
| Submission date |
Sep 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Gertz |
| E-mail(s) |
jgertz@hudsonalpha.com
|
| Organization name |
HudsonAlpha Institute
|
| Street address |
601 Genome Way
|
| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE32307 |
Transposon-based construction of strand-specific RNA-seq libraries |
|
| Relations |
| SRA |
SRX098300 |
| BioSample |
SAMN00723022 |
