|
| Status |
Public on Jul 03, 2018 |
| Title |
KO rep3 |
| Sample type |
SRA |
| |
|
| Source name |
KO, primary nephron progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: primary nephron progenitor cells
genotype: Dis3l2-/-
passages: 1
|
| Treatment protocol |
Cells derived from either Dis3l2+/+ or Dis3l2-/- embryos passaged once in culture before collection
|
| Growth protocol |
Primary nephron progenitor cells isolated accoding to protocol "A synthetic niche for nephron progenitor cells" (Brown et al 2015)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA collection was performed in well using miRNeasy Mini Kit with On-Column DNase Digestion (Qiagen) according to protocol
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequenced using 50 base pair single-end reads on an Illumia HiSeq2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
7_KO
|
| Data processing |
Reads were aligned to the mm10 reference genome with GENCODE M16 annotation using HISAT2 version 2.1.0 using default parameters
Read count per gene was generated by featureCounts
Differential expression analysis was performed on uniquely mapped reads with edgeR version 3.20.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including gene id, gene name, logFC, logCPM, LR, p-value, FDR, and cpm within each sample
|
| |
|
| Submission date |
May 19, 2018 |
| Last update date |
Jul 03, 2018 |
| Contact name |
Joshua Mendell |
| Organization name |
UT Southwestern Medical Center Dallas
|
| Department |
Molecular Biology
|
| Street address |
5323 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9148 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE114673 |
Gene expression profiling in Dis3l2-null and wild-type nephron progenitor cells |
|
| Relations |
| BioSample |
SAMN09227468 |
| SRA |
SRX4103429 |
