|
| Status |
Public on Oct 01, 2019 |
| Title |
WT4 |
| Sample type |
SRA |
| |
|
| Source name |
E12.5 Head
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Zcchc8+/+
strain: C57BL/6J
tissue: embryonic head
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole heads were preserved in RNAlater, Millipore-Sigma, and then homogenized using the Bullet Blender (Zirconium oxide beads). Total RNA was prepared from this homogenate
Truseq Stranded mRNA Library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data were generated by NovaSeq6000 using NovaSeq Control Software v1.4. BCL files were demultiplexed and converted to compressed fastq with bcl2fastq2.20.0 (Illumina’s current demultiplexer).
Reads were trimmed to 100bp after FastQC (v. 0.10.0) quality checking
The reads were aligned to the mm10 genome using topHat2 v.2.1.0
The aligned reads were assembled with CLASS v.2.1.7 to create transcript models (transfrags).
Transfrags were merged using Cuffmerge (v.2.2.1) and mapped to GENECODE v.M17
FPKM were calculated with Cuffdiff2 v.2.2.1
FPKM values were log2 converted and quantile normalized with Partek GS 7.0
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file (Cuffdiff_Annot_matrix.txt) provides the (Partek GS) Log2 quantile normalized FPKM values and annotations for all samples.
|
| |
|
| Submission date |
Feb 05, 2019 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Mary Armanios |
| E-mail(s) |
marmani1@jhmi.edu
|
| Organization name |
The Johns Hopkins University
|
| Department |
School of Medicine
|
| Lab |
Medical Oncology
|
| Street address |
401 North Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE126108 |
RNAseq of Zcchc8 mutant mouse embryonic heads |
|
| Relations |
| BioSample |
SAMN10874135 |
| SRA |
SRX5335988 |
