|
| Status |
Public on Oct 24, 2013 |
| Title |
MEFs+BAM_48hrs_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
transfection: infected with Ascl1, Brn2, Myt1l + dox
time: 48hrs
cell type: MEFs infected with Ascl1, Brn2, Myt1l after 48hrs dox
strain: C57BL/6
|
| Treatment protocol |
Lentivirus was produced following standard procedures, following transfection of TetO-FUW lentiviral backbones containing the respective cDNAs (available from us via Addgene) together with the 3rd generation packaging plasmids from the Trono laboratory (Dull et al., 1998). Media was changed 16h after transfection and viral supernatant collected after another 24h.
|
| Growth protocol |
Embryonic fibroblasts were isolated as previously described from the distal extremities of E14.5 homozygous TauEGFP mice embryos (Vierbuchen et al., 2010). iN cells were generated following the previously described protocol (Vierbuchen et al., 2010).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was purified with Trizol following supplier’s recommended method. Poly-A RNA was isolated from 0.5-3µg total RNA using the MicroPoly(A)Purist Kit (Ambion). Samples were processed according to the manufacturer’s protocol.
libraries were prepared following the dUTP protocol (Levin et al., 2010).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Paired-end reads were aligned to the mouse reference sequence NCBI Build 37/mm9 with the TopHat (v1.1.3) algorithm.
Expression levels of RefSeq annotated genes were calculated in unit of fragments per kilobase of exon model per million mapped fragments (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: The processed file is in txt format with expression levels of RefSeq genes calculated in RPKM.
|
| |
|
| Submission date |
Jan 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Dr. CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE43916 |
Hierarchical mechanisms for transcription factor-mediated reprogramming of fibroblasts to neurons |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX220740 |
| BioSample |
SAMN01907341 |
