|
| Status |
Public on Dec 12, 2017 |
| Title |
10X43_1_AAGCCAACGCGATT-1 |
| Sample type |
SRA |
| |
|
| Source name |
dentate gyrus, postnatal day 12
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: CD-1
genotype/variation: wild type
postnatal day: 12
tissue: dentate gyrus
cell cluster: Microglia
|
| Growth protocol |
Male and female wild type CD-1 mice (Charles River) at postnatal days 12, 16, 24, and 35 were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were sacrificed by an overdose of Isoflurane or Ketamin/Xylazine, followed by perfusion through the left ventricle with artificial cerebrospinal fluid, equilibrated in 95%O2/5%CO2 on ice or 4°C. The dentate gyrus was then microdissected from 300 μ m vibratome brain sections. Single-cell suspensions were prepared using the Papain kit (Worthington) with 25-35min enzymatic digestion followed by manual trituration using a BSA-coated p1000 pipette or fire-polished Pasteur pipettes. Sampling was carried out on two experimental days, each day pooling from male and female mice in a single experiment. The dentate gyrus of male (day 1 p35, day 2 p24) and female (day 1 p12, day 2 p16) mice were dissected and dissociated separately. Suspensions were pooled at equal ratios.
1000 cells/μl were resuspended in artificial cerebrospinal fluid and added to the Reverse transcription mix to aim for sampling of around 3500 cells. All downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing were carried out as instructed by the manufacturer (10X Genomics Chromium Single Cell Kit Version 1).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Processed data file: 10X_expression_data.tab.gz
|
| Data processing |
Processing was performed with the 10X Chromium cellranger pipeline version 1.1 using default settings
The Unique Molecular Identifier and cellular barcode corresponding to each read have been appended to the end of the read id in the fastq files, separated by an underscore.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: 10X_expression_data.tab: Tab-delimited text file of total RNA molecules in each cell.
|
| |
|
| Submission date |
Feb 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sten Linnarsson |
| Organization name |
Karolinska Institutet
|
| Department |
Medical Biochemistry and Biophysics
|
| Lab |
Molecular Neurobiology
|
| Street address |
Scheeles väg 1
|
| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE95315 |
Transcriptome analysis of single cells from the mouse dentate gyrus [10X] |
| GSE95753 |
Transcriptome analysis of single cells from the mouse dentate gyrus |
|
| Relations |
| BioSample |
SAMN06439752 |
| SRA |
SRX2600985 |
