 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 02, 2017 |
| Title |
SAM17865179 E15.5 |
| Sample type |
SRA |
| |
|
| Source name |
RNA from Medial Ganglionic Eminence
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Medial Ganglionic Eminence
age: E15.5
extendedphenotype: proliferating
subtype: pro3
nonneuralcelltype: NA
date: 20131218
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MGE tissues from mouse CD1 embryonic brains were dissected out from various embryonic ages. A single-cell suspension was prepared and then analyzed with C1 Single Cell Autoprep System per manufacturers’ recommended protocols (Fluidigm).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Cells with <2 million reads/cell, ≥5% mitochondrial reads, or <10% of annotated genes (~3,700) detected were discarded (and not part of this GEO series). Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
|
| |
|
| Submission date |
Feb 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Brad A Friedman |
| E-mail(s) |
friedmab@gene.com
|
| Organization name |
Genentech, Inc.
|
| Department |
Bioinformatics
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94133 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE94641 |
Single cell RNA expression of mouse embryonic basal forebrain |
|
| Relations |
| BioSample |
SAMN06310742 |
| SRA |
SRX2543257 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2480117_sample124.tsv.gz |
144.1 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
