|
| Status |
Public on Oct 12, 2020 |
| Title |
Neuronal nuclei Col_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
age (weeks): 5.5
strain: Phox2b-CFP
Sex: Male
tissue: Colon
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated using the NucleiEZ lysis buffer with modifications, as described in May-Zhang et al. FACS was performed to isolate neuronal nuclei and glia, which were gated for 7AAD+ and high intensity of CFP from the Phox2b-CFP reporter and collected into a 1.5-mL RNAse-free tube filled with 350 uL of RNA lysis buffer RLT from the RNeasy Micro kit.
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 mouse 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 |
GPL24247 |
| Series (2) |
| GSE153132 |
Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ [Mouse nuclei bulk RNA-Seq] |
| GSE153202 |
Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ |
|
| Relations |
| BioSample |
SAMN15356652 |
| SRA |
SRX8607556 |
