|
| Status |
Public on Jul 30, 2020 |
| Title |
WT_prog_4.5_HB_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Prominin-1 sorted neural progenitors (4 days)
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129
genotype/variation: wild type
cell status: d4.5 ESC differentiation
cell type: Prominin-1 sorted neural progenitors (4 days)
|
| Treatment protocol |
RA and SAG applied 0-3 DDC (days in differentiation conditions)
|
| Growth protocol |
Cells were grown in monolayer conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ZymoPureTM kit
Illumina TruSeq; polyA-selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
P1201_508
WT_Prog_4.5_Control-P1201_508
|
| Data processing |
Clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.2.38/RTA 1.18.61) with a 1x51 setup in RapidHighOutput mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
Reads were mapped with Tophat/2.0.4 to the Mouse genome assembly, build GRCm38 using default parameters settings.
Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
FPKMs for genes and transcripts were generated using cufflinks/2.1.1 on bamfiles with duplicates included.
Voom normalized logCPM values were obtained using voom function from R limma package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM, Counts and Voom normalized values for each sample
|
| |
|
| Submission date |
Apr 04, 2018 |
| Last update date |
Jul 30, 2020 |
| Contact name |
Johan Ericson |
| E-mail(s) |
johan.ericson@ki.se
|
| Organization name |
Karolinska Instituet
|
| Department |
Cell and Molecular Biology
|
| Lab |
Johan Ericson's Group
|
| Street address |
Solnavägen 9
|
| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE114640 |
Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d4.5, d5.5 and d6.5] |
|
| Relations |
| BioSample |
SAMN08863979 |
