|
| Status |
Public on Jul 27, 2015 |
| Title |
WT1_total_RNA |
| Sample type |
SRA |
| |
|
| Source name |
WT1_total_RNA
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
tissue: Bone Marrow
strain: C57BL/6J
|
| Growth protocol |
Mice were treated according to the University of Pennsylvania’s Animal Resources Center and IACUC protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
24,000 Flt3- LSK cells were sorted into Trizol and RNA was purified (Qiagen). Spike-in RNA (ERCC RNA Spike-In Mix, Life Technologies) was added following the manufacturer’s instructions.
Two types of sequencing libraries were prepared; one from polyA-selected RNA to analyze mRNAs, and one from total RNA to compare rRNA levels. mRNA was isolated from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). PolyA-selected mRNA was fragmented to average size of 300 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired end library using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit (Q32851) for Qubit and the size distribution was assessed using High Sensitivity DNA Kit (5067-462) for Bioanalyzer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads mapped to the combination reference of mouse genome (release mm9), ERCC transcripts and rDNA region through Tophat
Gene level read counts estimated by FeatureCounts for combination of Ensembl genes(release 66), ERCC transcripts and rRNA genes
Differentially expressed genes were called by edgeR
Genome_build: mm9 + ERCC + rDNA
Supplementary_files_format_and_content: text file, gene level read counts matrix
|
| |
|
| Submission date |
Apr 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Long Gao |
| E-mail(s) |
[email protected]
|
| Phone |
267-425-0053
|
| Organization name |
The Children’s Hospital of Philadelphia
|
| Lab |
Tan Lab
|
| Street address |
4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE67609 |
Runx1 deficiency decreases ribosome biogenesis and confers stress resistance to hematopoietic stem and progenitor cells |
|
| Relations |
| BioSample |
SAMN03462059 |
| SRA |
SRX978923 |
