|
| Status |
Public on Aug 21, 2024 |
| Title |
PATZ1_KO_ESC rep1 |
| Sample type |
SRA |
| |
|
| Source name |
E14 ESCs differentiated into cervical MNs
|
| Organism |
Mus musculus |
| Characteristics |
cell_type: Motor Neurons
genotype: Patz1 -/-
cell line: 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 NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to mm10 reference genome using tophat 2.1.1 and bowtie2 2.3.1
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.
Assembly: mm10
Supplementary files format and content: counts in txt format
|
| |
|
| Submission date |
Apr 24, 2023 |
| Last update date |
Aug 21, 2024 |
| Contact name |
Danny Reinberg |
| Organization name |
University of Miami
|
| Department |
Sylvester Cancer Center/Human Genetics
|
| Lab |
Reinberg Lab
|
| Street address |
1501 NW 10th Ave
|
| City |
Miami |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE230478 |
Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [RNA-Seq2] |
| GSE230482 |
Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries |
|
| Relations |
| BioSample |
SAMN34356751 |
| SRA |
SRX20088888 |
