|
| Status |
Public on Jul 18, 2019 |
| Title |
disease rep2 [W_006] |
| Sample type |
SRA |
| |
|
| Source name |
disease_endometrial tissue
|
| Organism |
Homo sapiens |
| Characteristics |
group: disease
tissue: endometrial tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Qiagen RNeasy kit following storage in RNAlater
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded library preparation kit. The method involves mRNA enrichment from total RNA followed by RNA fragmentation and conversion to double-stranded cDNA using random hexamers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
checked the quality of the data using FastQC
remove reads with low‐quality bases, adapter sequences, and other contaminating sequences using Cutadapt
Bowtie2 was used to build the index of reference genome
TopHat was used to map the short sequence reads to the reference genome
HTSeq was applied to generate the read count data
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes the raw read counts for all samples
|
| |
|
| Submission date |
Jul 09, 2019 |
| Last update date |
Jul 18, 2019 |
| Contact name |
Trupti Joshi |
| E-mail(s) |
joshitr@health.missouri.edu
|
| Organization name |
University of Missouri
|
| Street address |
NW 502, One Hospital Drive
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65212 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE134056 |
Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data [Transcriptomics] |
|
| Relations |
| BioSample |
SAMN12239239 |
| SRA |
SRX6422865 |
