|
| Status |
Public on Feb 24, 2020 |
| Title |
Sox9eGFP Low HFD RNA-seq Rep #1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: small intestine
strain: C57BL/6J
diet: HFD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Clonetech SMARTer Ultra Low Input library preparation kit combined with Nextera XT DNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC181
|
| Data processing |
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9 and dm3 for mouse and fruit fly small RNA-seq, mm10 for mouse RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.
|
| |
|
| Submission date |
Aug 20, 2018 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Praveen Sethupathy |
| Organization name |
Cornell University
|
| Lab |
Dr. Sethupathy Lab
|
| Street address |
Cornell University College of Veterinary Medicine, Box 17
|
| City |
Ithica |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE118814 |
MicroRNA-7 regulates the plasticity of the enteroendocrine lineage |
|
| Relations |
| BioSample |
SAMN09866501 |
| SRA |
SRX4580953 |
