|
| Status |
Public on Jan 30, 2013 |
| Title |
miPS MCV8.1, fully reprogrammed MEF (iPS) |
| Sample type |
SRA |
| |
|
| Source name |
MCV8.1
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/svJae x C57BL/6
tissue: induced pluripotent stem cell
age: reprogrammed cell
genotype: Oct4-GFP, retrovirally-transduced with Oct4, Sox2, c-myc and Klf4
|
| Treatment protocol |
No treatment was applied to the cell lines used to identify candidate lincRNAs.
|
| Growth protocol |
Mouse ESCs and iPS cells were cultured on irradiated MEFs using standard techniques. Cell were pre-plated for 30 minutes prior to harvesting to remove MEFs. 11.3 and 11.5 cells were cultured in feeder-free conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol® Reagent according the manufacturer’s instructions. Sequencing libraries were prepared according to Illumina RNA-Seq library kit with minor modifications. Briefly, mRNA was isolated using Dynabeads® mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation. First and second strand synthesis were performed followed by end repair, A-tailing, paired end adapter ligation and size selection on agarose gels. 200-400 bp dsDNA was enriched by 15 cycles of PCR with Phusion® High-Fidelity DNA Polymerase (NEB) followed by gel purification of ~250 bp fragments from the amplified material. Amplified libraries were sequenced on an Illumina GAII or GAIIx sequencer, alternatively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Generated as described in http://www.ncbi.nlm.nih.gov/pubmed/18509334
|
| Data processing |
Illumina Offline BaseCaller1.9.3 software used for basecalling.
Sequence reads were mapped to mm9 whole genome using Tophat 1.3 with the following parameters --min-anchor-length 6 --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --max-multihits 50 --no-novel-juncs --no-novel-indels --library-type fr-unstranded
Gene expression was calculated as Reads per Kilobase of modeled exon per Million mapped reads (RPKM) using rsem
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file that includes RPKM values for each Sample.
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Laurie A Boyer |
| E-mail(s) |
lboyer@mit.edu
|
| Phone |
617 324-3335
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Biology
|
| Lab |
Boyer
|
| Street address |
77 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE39656 |
Braveheart is a long non-coding RNA necessary for cardiac lineage commitment |
|
| Relations |
| SRA |
SRX185769 |
| BioSample |
SAMN01163785 |
