|
| Status |
Public on May 06, 2015 |
| Title |
Epiblast-AP |
| Sample type |
SRA |
| |
|
| Source name |
E6.5 epiblast tissue anterior-proximal
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E6.5 epiblast
passages: N/A
strain: ICRxICR
|
| Growth protocol |
EpiSCs were grown on MEFs in N2B27 media containing 12ng/ml FGF2 and 20ng/ml Activin-A supplemented with 20% KSR; rsEpiSCs were grown on MEFs in N2B27 media containing 20ng/ml and IWR1 2.5uM; Human ESCs (H1 & H9) were grown on matrigel-coated dishes in mTeSR1 media; Human rsESCs (H1 & H9) and Chimp rsiPSCs were grown on Matrigel-coated plates in modified mTeSR1 media containing 20ng/ml FGF2 and 2.5uM IWR1; Rhesus ORMES23 rsESCs were grown on MEFs in modified N2B27 media containing 20ng/ml FGF2 and 2.5uM IWR1, MEFs were removed before RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of all samples was extracted using RNeasy Mini Kit (Qiagen) per manufacturer's instructions.
RNA libraries were prepared for sequencing using strand-specific Illumina TruSeq kits per the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
E6.5 epiblast tissue anterior-proximal RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-invivo.txt.gz
|
| Data processing |
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the mouse (mm9) or human (hg19) genomes with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis.
Reads Per Kilobase of exon per million mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text file. Columns: (1) RefSeq acc, (2) chr, (3) start, (4) end, (5) strand, (6) length, (7) copies, (8) annotation, (9 to the end) FPKM.
|
| |
|
| Submission date |
Nov 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Benner |
| E-mail(s) |
cbenner@ucsd.edu
|
| Organization name |
University of California, San Diego (UCSD)
|
| Department |
Medicine
|
| Street address |
9500 Gilman Dr. MC 0640
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0640 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE60603 |
An alternative pluripotent state confers interspecies chimaeric competency [RNA-Seq] |
| GSE60605 |
An alternative pluripotent state confers interspecies chimaeric competency |
|
| Relations |
| BioSample |
SAMN03216783 |
| SRA |
SRX765899 |
