|
| Status |
Public on Aug 28, 2013 |
| Title |
BSO36_NuGEN |
| Sample type |
SRA |
| |
|
| Source name |
human mammary epithelial cell
|
| Organism |
Homo sapiens |
| Characteristics |
involution: No
cell type: human mammary epithelial cell
rna preparation: NuGEN Ovation
|
| Growth protocol |
All cell lines were grown under conditions recommended by ATCC and RNA was extracted from mid log phase cultures at low passage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from mid log phase cultures at low passage (P1 or P2) using Triazol kit (Invitrogen)
For Illumina libraries, 5ug total RNA were processed according to the mRNA Seq Sample Preparation Kit protocol (part number 1004898 Rev A), with the 300bp gel fragment eluted and purified for sequencing. For NuGEN libraries, 500-800pg total RNA were amplified and converted to cDNA using NuGEN’s Ovation RNA-Seq kit. Following amplification, 4.6-5.0ug cDNA was fragmented to ~200bps using Covaris S2 and the fragmentation parameters described in the NuGEN ENCORE NGS library preparation protocol. The remainder of the library preparation followed manufacturer’s protocol as described in NGS Library System I and Multiplex System, Part no. 300.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls made by standard Illumina pipleline (Bustard)
The pair end reads were aligned to the human genome build 37.1 using TopHat (1.4.0) and Bowtie (0.12.7). HTSeq (0.5.3p3) was used to perform gene counting while BEDTools (2.7.1) was used to count the reads mapping to individual exons according to RefSeq gene annotations (Feb 2009, GRCh37/hg19) with 23,113 genes.
Genome_build: hg19
Supplementary_files_format_and_content: text; gene level expression count
|
| |
|
| Submission date |
Jun 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhifu Sun |
| Organization name |
Mayo Clinic
|
| Department |
HSR-BSI
|
| Street address |
200 1st ST SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE47933 |
Impact of library preparation on downstream analysis and interpretation of RNA-seq data: comparison between Illumina PolyA and NuGEN Ovation protocol |
|
| Relations |
| BioSample |
SAMN02203526 |
| SRA |
SRX305398 |
