|
| Status |
Public on Feb 23, 2014 |
| Title |
KO_3 |
| Sample type |
SRA |
| |
|
| Source name |
TER119+ E14.5 fetal liver cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ
genotype: Klf3-/-
|
| Treatment protocol |
TER119+ cells were purified from E14.5 fetal liver using Magnetic Activated Cell Sorting with Anti-TER119 MicroBeads (Miltenyi)
|
| Growth protocol |
All mice were housed in standard University of NSW facilities, under SPF conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using TRI-Reagent, according to manufacturer’s guidelines (Sigma-Aldrich). RNA samples were further purified using RNeasy columns (Qiagen)
Libraries were prepared using 1µg of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) according to the manufacturer’s instructions.
The six libraries were multiplexed into two lanes using sample specific adapters such that there were three samples per lane. 100 bp paired end reads were sequenced using TruSeq v3 SBS reagents on the HiSeq 2000 (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
"Stringent" - Reads were aligned to the mm10 Mus musculus genome using tophat2 (v2.0.4) using the default settings except for the following (-r -40 --segment-length 50 --coverage-search --segment-mismatches 0 -g 50 --genome-read-mismatches 0 --read-mismatches 0 -I 200000 --no-discordant --no-mixed --b2-L 30 --b2-D 10000 --b2-R 100 -n 0 -M) OR;
"Routine" - Reads were aligned to the mm10 Mus musculus genome using tophat2 (v2.0.4) using the default settings except for the following (--no-discordant -M --no-coverage-search --microexon-search -n 3 --genome-read-mismatches 3 --read-mismatches 3 --b2-sensitive -G)
Transcripts were assembled using Cufflinks v2.0.2 and the mm10 annotations were included
Transcripts across all replicates were merged using cuffmerge and differential expression analysis was performed pair-wise on the groups using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files giving results of differential expresison and statistical analysis
|
| |
|
| Submission date |
Sep 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jon Burdach |
| Organization name |
University of New South Wales
|
| Department |
BABS
|
| Street address |
UNSW
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE50554 |
RNA-Seq analysis of KLF3 knockout E14.5 TER119+ (erythroid) murine fetal liver cells |
|
| Relations |
| BioSample |
SAMN02343491 |
| SRA |
SRX343146 |
