|
| Status |
Public on Jul 03, 2024 |
| Title |
KLF1 +/- mRNAseq rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
14.5DPC fetal liver
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: 14.5DPC
tissue: Fetal Liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fetal Livers were homogenized and washed in PBS. Trizol reagent was used to extract total RNA.
Total RNA was treated with GLOBINclear kit for mouse (ThermoFisher Scientific; AM1981). mRNA was then purified from treated RNA using DynaBeads mRNA Direct purification Kit (Thermofisher Scientific, #61012). Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific; #4479789) was used to prepare libraries for sequencing on the Ion Proton™ System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
ChIP-Seq:
Base calling was performed with RTAv2
Bowtie2 was used to mapped PE sequencing reads with default parameters to the reference genome (mm9)
Duplicate reads were removed using Picard with the MarkDuplicates function
ChIP-seq peaks were called with MACS2 using uniquely mapped ChIP and input sequence alignments.
---------------
RNA-Seq
Base calling was performed with Torrent Suite v4.0.1
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -g 3, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: -o 1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between replicate groups was performed with Cuffdiff2 using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited genelist of FPKM output from CuffDiff2
Supplementary_files_format_and_content: excel file of peaks called from MACS2 for both wildtype and mutant ChIPseq
|
| |
|
| Submission date |
Jan 31, 2017 |
| Last update date |
Jul 03, 2024 |
| Contact name |
Stephen Huang |
| Organization name |
University of Queensland
|
| Department |
Mater Research institute
|
| Lab |
Cancer Genomics
|
| Street address |
37 Kent Street Woolloongabba
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4102 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE94351 |
Mutations in linker-2 of KLF1 impair expression of membrane transporters and cytoskeletal proteins causing hemolysis |
|
| Relations |
| BioSample |
SAMN06285638 |
| SRA |
SRX2530439 |
