|
| Status |
Public on Jun 01, 2017 |
| Title |
Day 4 replicate 4 |
| Sample type |
SRA |
| |
|
| Source name |
cultured rat embryonic neurons 4 days after plating
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
developemental stage: E18
tissue: Brain cortex
cell type: Embryonic cortical neurons
co-cultured with: primary rat astrocytes from P0-2 rats
time point: 4 days after plating
|
| Growth protocol |
Cortical neurons were derived from E18 Sprague Dawley rat cortex, and were plated at the density of 100-150 cells/mm2. The medium used for plating was a combination of fresh B27 medium (neurobasal medium supplemented with 2% B27 and 1% Glutamax) and B27 medium conditioned by astrocytes.
Astrocytes were derived from P0-2 Sprague Dawley rat cortex, and were grown for 7-8 days before being frozen for future use. They were then thawed and further grown for another 5-6 days before being combined with neurons as co-culture, or used for B27 medium conditioning.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 1, 4, 8, 16, and 24 DIV cultures by using the Qiagen RNeasy Micro Kit (Qiagen, 74004)
RNA was subjected to whole-transcriptome amplification using NuGEN RNAseq v2 System followed by fragmentation to 200bp with a Diagenode Bioruptor Pico sonicator, The resulting fragments were then used to make bar-coded libraries using NuGEN Ovation Rapid DR Multiplex System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA harvested from cultured rat embryonic neurons 4 days after plating
D4-4-SLX-9155.L2DRBC07.bam-FPKM
|
| Data processing |
Reads were aligned to the Rnor5.0/Ensembl V75 transcriptome using Tophat v2.0.8 with default parameters
Counts and differential gene expression were determined using CuffLinks v2.2.1 using default parameters
Genome_build: Rnor 5.0
Supplementary_files_format_and_content: Fastq files for raw data and FPKM values in tab-delimted txt format
|
| |
|
| Submission date |
Dec 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Yee Hong Lam |
| E-mail(s) |
yhbl2@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Metabolic Research Laboratories
|
| Street address |
Box 289 Addenbookes Hospital, Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE92856 |
Gene expression profiling of cultured embryonic rat cortical neurons |
|
| Relations |
| BioSample |
SAMN06176798 |
| SRA |
SRX2441433 |
