|
| Status |
Public on Dec 07, 2016 |
| Title |
24h RNA-Seq Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
ES-derived embryoid bodies with induced transcription factors
|
| Organism |
Mus musculus |
| Characteristics |
strain: Ainv15(iNgn2.Isl1.Lhx3.V5)
cell type: Embryoid Bodies
|
| Treatment protocol |
To obtain Embryoid bodies (EBs) ESC were trypsinized (Gibco) and seeded in AK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout SR (vol/vol) (Gibco), Pen/Strep (Gibco), 2mM L-glutamine and 0.1 mM 2-mercaptoethanol) (day -2). After 2 days, EBs were passed 1:2 and the inducible cassette was induced by adding 3 µg/ml of Doxycycline (Sigma) to the culture medium (EBs 0h).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected at different time points after NIL induction and RNA isolated using TRIzol LS (Life Technologies) followed by purification using Qiagen RNAeasy kit
RNA-Seq libraries were prepared using Illumina TruSeq RNA library preparation kit v2. Fifty base pair single-end sequencing was performed using Illumina HiSeq-2500 at the NYU Genome Core facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling conversion to fastq files was performed using bcl2fastq
Expression was quantified from RNA-seq using the Gencode (Mudge and Harrow, 2015) mm10 transcriptome (vM3) and RSEM (parameters: --output-genome-bam –forward-prob=0 –calc-ci) (Li and Dewey, 2011). RSEM was set to use bowtie1 for read alignments (Langmead et al., 2009).
Genome_build: mm10
Supplementary_files_format_and_content: output files from RSEM including counts, FPKM and TPM values per gene (Gencode mm10 vM3 transcriptome)
|
| |
|
| Submission date |
Apr 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaun Mahony |
| E-mail(s) |
mahony@psu.edu
|
| Phone |
814-865-3008
|
| Organization name |
Penn State University
|
| Department |
Biochemistry & Molecular Biology
|
| Lab |
Shaun Mahony
|
| Street address |
404 South Frear Bldg
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE80483 |
A multi-step transcriptional and chromatin cascade underlies motor neuron programming |
| GSE80561 |
A multi-step transcriptional and chromatin cascade underlies motor neuron programming (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN04884723 |
| SRA |
SRX1719773 |
