|
| Status |
Public on May 21, 2015 |
| Title |
HIP_7 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus; Pyramidal neuron
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: embryonic day 18
tissue: Hippocampus
cell type: Pyramidal neuron
|
| Growth protocol |
Primary cultures of hippocampal and cortical neurons were plated at 100,000 per ml in neurobasal medium (Invitrogen) with B-27 supplement (Sigma) on 12-mm round German Spiegelglas coverslips (Bellco Glass) and grown for 14 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We identified pyramidal neurons by cell morphology, isolated single cells by aspiration using a wide-bore pipette, deposited collected material into an eppendorf tube and froze immediately at -20C until storage at -80C. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq v2 system according to manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
30H
|
| Data processing |
genome_build: mm9
genome_build: rn5
Illumina Casava 1.8.1 and 1.8.2 software used for basecalling.
We trimmed reads for adapter and poly-A contamination using in-house software before aligning to the mouse genome and transcriptome using RNA-Seq Unified Mapper (versions 2.0.2_06 and 2.0.3_04) and mouse genome build mm9 (mouse) or to the rat genome using STAR and rat genome build rn5. We required three or less mismatches per 100 bases.
Using uniquely aligned reads to RefSeq annotations downloaded from UCSC genome browser, we assigned read counts to genes using HTSeq and htseq-count. Only exonic reads were counted, with overlap assigned using the intersection non-empty method.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each gene
|
| |
|
| Submission date |
Apr 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
|
| Department |
Biology
|
| Lab |
Junhyong Kim
|
| Street address |
433 S University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE56638 |
Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation |
|
| Relations |
| BioSample |
SAMN02725866 |
| SRA |
SRX515395 |
