|
| Status |
Public on Mar 28, 2013 |
| Title |
placenta RNA rep1 |
| Sample type |
SRA |
| |
|
| Source name |
placenta
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta from full-term pregnancy
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the NuGEN Ovation RNA-Seq System. Indexed adapters were added using the NuGEN Encore NGS Library System I.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing index was in first 4 bases of sequencing read. For raw fastq files, first four bases were removed and separate fastq files were made for each indexed replicate.
Reads were mapped to the hg18 version of the genome using TopHat (version 1). Parameters: --library-type fr-unstranded –GTF –butterfly-search –no-novel-juncs --prefilter-multihits
Cufflinks was used to assemble the mapped reads into transcripts, omitting reads that did not align to known transcripts. Parameters: --library-type fr-unstranded – GTF –frag-bias-correct –multi-read-correct –frag-len-mean 390 –compatible-hits-norm
Genome_build: hg18
Supplementary_files_format_and_content: fpkm_tracking file from Cufflinks
|
| |
|
| Submission date |
Jul 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Janine LaSalle |
| E-mail(s) |
jmlasalle@ucdavis.edu
|
| Organization name |
UC Davis
|
| Street address |
Medical Microbiology and Immunology
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE39776 |
Examination of gene expression in human placenta using RNA-seq |
| GSE39777 |
Comparison of DNA methylation in human tissues |
|
| Relations |
| SRA |
SRX172467 |
| BioSample |
SAMN01096254 |
