|
| Status |
Public on Jun 20, 2024 |
| Title |
15_ARM-083 |
| Sample type |
SRA |
| |
|
| Source name |
rectal biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: rectal biopsy
race group: NonBlack
age: 45
age group: Adult
msm: MSM
p24 logauc: --
hiv status: --
sti status: --
batch: Batch2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from two rectal biopsy pinches for each patient using the RNeasy Micro kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Alignment was performed using STAR version 2.5.2b
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count
Assembly: GRCh38, Emsembl annotation v86
Supplementary files format and content: comma delimited text file containing ensembl ID, gene symbol, gene description and raw read counts for each sample (in columns) for each annotated transcript (in rows).
|
| |
|
| Submission date |
Jun 20, 2024 |
| Last update date |
Jun 21, 2024 |
| 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 |
GPL24676 |
| Series (1) |
| GSE270349 |
Transcriptomic data from a clinical cohort of men who have sex with men (MSM) and controls. |
|
| Relations |
| SRA |
SRX24993399 |
| BioSample |
SAMN41941396 |
