|
| Status |
Public on Feb 06, 2022 |
| Title |
RNA-seq_WT_E14_ESC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
genotype: wild type
developmental stage: E14
|
| Growth protocol |
mESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)). For motor neuron (MN) differentiation, the previously described protocol in Narendra et. al. (2015) was applied. Briefly, ESCs were differentiated into embryoid bodies in 2 days (Day 0) 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). Medium was exchanged on Day 2 of differentiation, and further patterning of embryoid bodies was induced by supplementing the ANDFK 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 RNAeasy Plus Mini kit (Qiagen), and 1ug RNA was used for library preparation.
RNA was used to prepare automated TruSeq (Illumina) stranded RNAseq libraries by using RiboZero Gold library prepation according to manufacturer's protocols by NYU Genome Technology Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter cells
|
| Data processing |
Reads were aligned to mm10 reference genome using tophat 2.0.9 and bowtie2 2.1.0
Reads were assigned to the UCSC mm10 gene annotation
Counts were obtained by using featureCounts v1.6.2
Normalized differential expression (taking into account biological replicates) was calculated by using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: counts in txt format
|
| |
|
| Submission date |
Aug 30, 2020 |
| Last update date |
Feb 06, 2022 |
| Contact name |
Danny Reinberg |
| E-mail(s) |
Danny.Reinberg@nyulangone.org
|
| Phone |
212-263-9036
|
| Organization name |
New York University School of Medicine
|
| Department |
Biochemistry
|
| Lab |
Reinberg Lab
|
| Street address |
522 First Avenue, 2nd floor, Room 211
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE157137 |
CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters [MAZ KO] |
| GSE157139 |
CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters |
|
| Relations |
| BioSample |
SAMN15942068 |
| SRA |
SRX9036160 |
