|
| Status |
Public on Feb 26, 2015 |
| Title |
Day4.Δ5|6.b1 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Differentiating Motor Neurons (Day 4 post RA/SAG)
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Δ5|6
time point: Day 4
|
| Growth protocol |
mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). ESCs were differentiated in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 of differentiation. Patterning of embryoid bodies was induced by supplementing the media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from cells with TRIzol (Invitrogen)
PolyA+ RNA was isolated using Dynabeads Oligo(dT)25 (Invitrogen) beads and converted into dsDNA using the dUTP method (Parkhomchuk et al., 2009). DNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR) using Q5 polymerase (NEB M0530) to generate strand-specific libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
mapped to mm9 with BOWTIE -m40 -v2
reads were assigned to the ENSEMBL annotation using DEGseq
Normalized differential expression (taking into account biological replicates) was calculated using Deseq
Genome_build: mm9
Supplementary_files_format_and_content: Raw read count and RPKM matching the ENSEMBL annotation
|
| |
|
| Submission date |
Aug 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Danny Reinberg |
| E-mail(s) |
reinbd01@nyumc.org
|
| Phone |
212-263-9036
|
| Organization name |
NYU School of Medicine / HHMI
|
| Street address |
522 First Avenue, 2nd floor Rm 211
|
| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE60226 |
CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [RNA-Seq] |
| GSE60240 |
CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation |
|
| Relations |
| BioSample |
SAMN02978979 |
| SRA |
SRX672301 |
