NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1074356 Query DataSets for GSM1074356
Status Public on Oct 24, 2013
Title MEFs+BAM_22days_Rep2
Sample type SRA
 
Source name embryonic fibroblasts
Organism Mus musculus
Characteristics transfection: infected with Ascl1, Brn2, Myt1l + dox
time: 22 days
cell type: MEFs infected with Ascl1, Brn2, Myt1l after 22 days 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 SRX220744
BioSample SAMN01907345

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap