|
| Status |
Public on Apr 01, 2012 |
| Title |
WT library 3 |
| Sample type |
SRA |
| |
|
| Source name |
Total Fetal Liver Klf1+/+
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
genotype/variation: wildtype
tissue: Fetal liver
developmental stage: Embryonic day 14.5
|
| Growth protocol |
Fetal livers were collected from E14.5 timed matings (Klf1+/- x Klf1+/-) by dissection, mechanically dissociated and passed through a 40 micron cell strainer to obtain a single cell suspension. Fetal livers were collected from 3 Klf1-/- embryos and 3 Klf1+/+ embryos from 2 independent litters and genotypes confirmed by PCR.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected from homogenized E14.5 fetal livers using TRIzol (Invitrogen) and treated with amplification grade DNaseI (Invitrogen). 12μg of total RNA for each sample was treated with the mouse GlobinClear kit (Ambion) to remove the majority of globin RNA. Libraries were prepared from this RNA starting with 8μg per sample and using the mRNA-seq Sample Prep Kit (Illumina) as per recommended instructions. Cluster generation and sequencing was performed as per standard Illumina GAIIx protocols to generate single end reads of 76bp. Each library was sequenced in an individual lane of the GAIIx flow cell. A single Klf1+/+ library (WT library 3) was sequenced to approximately twice the depth by generating two lanes of sequence.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
s_1_8.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC (ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/mm9.ebwt.zip) to generate six BAM files individually using Tophat-1.3.1 (http://tophat.cbcb.umd.edu/downloads/).
|
| |
|
| Submission date |
Nov 28, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Robert Tallack |
| E-mail(s) |
m.tallack@imb.uq.edu.au
|
| Phone |
+61 7 3346 2357
|
| Organization name |
Institute for Molecular Bioscience, The University of Queensland
|
| Lab |
Perkins
|
| Street address |
Services Road
|
| City |
St Lucia |
| State/province |
QLD |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE33979 |
Novel roles for Klf1 in regulating the erythroid transcriptome revealed by mRNA-seq |
|
| Relations |
| SRA |
SRX109325 |
| BioSample |
SAMN00760829 |
