|
| Status |
Public on Mar 27, 2020 |
| Title |
Sox9_2 |
| Sample type |
SRA |
| |
|
| Source name |
Dissociated, FAC-sorted primary embryonic neural progenitors_Sox9
|
| Organism |
Mus musculus |
| Characteristics |
strain: Tis21-CreERT2 mouse line
genotype/variation: Sox9 constructs
age: Embryonic day 15.5
tissue: Brain
cell type: dissociated, FAC-sorted primary embryonic neural progenitors
|
| Treatment protocol |
Embryonic noecortices were dissected and dissociated. RFP expressing cells were sorted by FACS.
|
| Growth protocol |
Embryonic neocortex of E13.5, Tis21-CreERT2 embryos were in utero electroporated with either control or Sox9 constructs. The embryos were collected after 48 hours (at E15.5).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from sorted cells was extracted using the QIAGEN RNeasy Micro kit according to the manufacturer’s protocol. cDNA synthesis was performed with SmartScribe reverse transcriptase (Clontech), universal poly-dT primers and template switching oligos. Purified cDNA was amplified with Advantage 2 DNA Polymerase in 12 cycles, and subjected to ultrasonic shearing with Covaris S2.
Standard Illumina fragment libraries were prepared using NEBnext chemistries (New England Biolabs). Library preparation consisted of fragment end-repair, A-tailing and ligation to indexed Illumina TruSeq adapters, followed by a universally primed PCR amplification of 15 cycles. Then, libraries were purified using XP beads (Beckman Coulter) and quantified by qPCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sox9 - biological replicate 2
|
| Data processing |
Basecalling was performed with bcl2fastq 2.17.1.14
Reads were mapped using STAR v2.5.2b (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Abundance estimation was performed with STAR (--quantMode GeneCounts)
Genome_build: GRCm38, Ensembl v70
Supplementary_files_format_and_content: Raw counts and FPKM normalized expression values
|
| |
|
| Submission date |
Jul 11, 2019 |
| Last update date |
May 16, 2022 |
| Contact name |
Scientific Computing Facility |
| Organization name |
MPI-CBG
|
| Street address |
Pfotenhauerstrasse 108
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE134162 |
Extracellular matrix-inducing Sox9 orchestrates basal progenitor proliferation and gliogenesis in developing neocortex |
|
| Relations |
| BioSample |
SAMN12256403 |
| SRA |
SRX6432606 |
