|
| Status |
Public on Oct 12, 2020 |
| Title |
VU13_Col_R3 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Female
race: Caucasian
age: 33
sequencer: NovaSeq 6000
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Micro® kit (Ambion) as described in May-Zhang et al. Jove 2018. Briefly, 1-3 Arcturus XT laser capture caps were pooled for each sample after collecting sufficient quantities of enteric ganglia. Lysates were incubated at 26C for 30 min in 250uL of Buffer RLT with repeated brief vortexing. Lysates were frozen at -80C and stored for up to 2 months before isolating RNA.
cDNA libraries were prepared using the Takara SMARTer kit according to llumina's instructions. Libraries were sequenced using the NovaSeq as 1x100bp single-end reads. Each sample had a mean depth of approximately 138 million reads and a mean alignment rate of 99.01%.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software
RNA-Seq reads were then aligned to their respective Ensembl release 76 human or mouse top-level assemblies with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned, unambiguous reads by Subread:featureCount version 1.4.5
Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.13.
Sequencing performance was then assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
Genome_build: Ensembl release 76 human assembly
Supplementary_files_format_and_content: counts matrix
|
| |
|
| Submission date |
Jun 24, 2020 |
| Last update date |
Oct 12, 2020 |
| Contact name |
E Michelle Southard-Smith |
| E-mail(s) |
michelle.southard-smith@vanderbilt.edu
|
| Phone |
615-293-4236
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Medicine, Genetic Medicine
|
| Street address |
2215 Garland Ave,
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE153198 |
Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ [Human Enteric Ganglia] |
| GSE153202 |
Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ |
|
| Relations |
| BioSample |
SAMN15361736 |
| SRA |
SRX8610801 |
