|
| Status |
Public on Jun 19, 2017 |
| Title |
100-19_exp_2 MSM after engaging in CRAI <24 hours prior |
| Sample type |
SRA |
| |
|
| Source name |
100-19_exp_2
|
| Organism |
Homo sapiens |
| Characteristics |
experimental group: exp
visit: 2
tissue: rectal biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using RNAeasy Mini Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA nano Kit, Agilent, USA)
Libraries were prepared using the Illumina TruSeq mRNA protocol. Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell. Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to hg19 genome assembly with the STAR (v2.4.0g1) aligner args: --outFilterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile refGene.gtf --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G refGene.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was calculated with Cuffdiff (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Jun 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE83245 |
The rectal mucosal transcriptome of men who have sex with men (MSM) engaging in condomless receptive anal intercourse (CRAI) compared with men who have never engaged in anal intercourse (controls) |
|
| Relations |
| BioSample |
SAMN05230238 |
| SRA |
SRX1837865 |
