|
| Status |
Public on Mar 21, 2023 |
| Title |
4_4-CFAR_14-83527-004 |
| Sample type |
SRA |
| |
|
| Source name |
rectal pinch biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: rectal mucosa
donor id: 14-83527-004
treatmentgroup: new
alttreatmentgroup: TGW
|
| Treatment protocol |
Biopsies were stored at -80deg in RNAlater media before extraction.
|
| Growth protocol |
Rectal mucosal tissue biopsies were obtained via rigid sigmoidoscopy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After thaw and wash, cell pellets were resuspended in RNAzolRT prior to RNA extraction. Purified RNA was used for transcriptome analysis. Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform.
Libraries were sequenced on an Illumina HiSeq 3000 system in 101-base single-read
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Reads were aligned to the Human Reference Genome Sequence and transcripts annotated with Genome Reference Consortium Build 38 (GRCh38) using STAR software (v2·5·2b).
Unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.5.0
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Dec 10, 2019 |
| Last update date |
Mar 21, 2023 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
[email protected]
|
| 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 |
GPL21290 |
| Series (1) |
| GSE141785 |
Characterization of a Distinct Rectal Mucosal Transcriptome among Transgender Women utilizing Cross-Sex Hormone Therapy |
|
| Relations |
| BioSample |
SAMN13527018 |
| SRA |
SRX7320058 |
