|
| Status |
Public on Apr 30, 2014 |
| Title |
Total RNA 2 |
| Sample type |
SRA |
| |
|
| Source name |
E14 mESCs
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: 129/Ola
genotype: wt
sample type: Total RNA
antibody: none
cell type: E14 mESCs
|
| Growth protocol |
E14 mESCs were cultured in 15% FBS, DMEM + 1000U/ml LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cytoplasmic extracts were prepared via cold hypotonic lysis, and RNA/RNA binding protein complexes were immunoprecipitated (RIP) followed by extraction of co-isolated RNAs. As a control, RIP procedure was conducted using a non-specific rabbit IgG. Two E14 Total RNA preparations were sequenced to gauge gene expression levels prior to RIP. Isolated RNAs were processed according to manufacturer's instructions for Illumina's TruSeq RNA Prep kit. Briefly, RNA is fragmented at 94C to generate lengths of approximately 200nts. The fragments are reverse transcribed to double stranded DNA using random hexamer primers. Ends were blunted, adenylated and ligated to Illumina adapters. Fragments were gel separated and bands corresponding to 350bps were isolated for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecaller software: RTA 1.13.48.0, Pipeline and conversion to FASTQ format: CASAVA 1.8.2
Sequencing reads were trimmed of first 13nts to remove random hexamer priming bias
Trimmed reads were aligned to a mm9 transcript annotation containing only protein coding genes using Bowtie (v. 1.1.2) using default paramters
FPKM measurements were generated by eXpress (v. 1.1.1) using default parameters (see Roberts A. and Pachter L., in submission)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and other abundance statistics for each transcript annotation
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Frederick E Tan |
| E-mail(s) |
ftan@caltech.edu
|
| Phone |
626-395-5969
|
| Organization name |
California Institute of Technology
|
| Department |
Biology and Applied Physics
|
| Lab |
Michael Elowitz
|
| Street address |
1200 E. California Blvd, M/C 114-96
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE40104 |
High-throughput sequencing of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) targets |
|
| Relations |
| SRA |
SRX176591 |
| BioSample |
SAMN01113181 |
