|
| Status |
Public on Jul 05, 2016 |
| Title |
1_5c |
| Sample type |
SRA |
| |
|
| Source name |
neurons
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cervical spinal cord
cell number: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction from LCM dissected motor neurons, the Arcturus PicoPure RNA Isolation Kit was used. For other samples, cells are diectly picked after dissociation and deposited into lyssis buffer. No RNA extraction is conducted.The cell lysis is proceed directly to library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mouse_LCM_FPKM_table.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling
RNA-seq reads of mouse and human samples were separately mapped to the mouse reference genome (mm10) and human reference genome (hg38) using STAR (version 2.4.1) with parameter --outSAMstrandField intronMotif.
Expression of genes for each sample was quantified and normalized using Cufflinks and Cuffnorm (version 2.2.1) with parameter -library-norm-method geometric.
Genome_build: mm10 for mouse samples, hg38 for human samples
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Jan 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Eva Hedlund |
| E-mail(s) |
eva.hedlund@dbb.su.se
|
| Phone |
0046761130911
|
| Organization name |
Stockholm University
|
| Department |
Department of Biochemistry and Biophysics
|
| Lab |
Hedlund
|
| Street address |
Svante Arrhenius v. 16C
|
| City |
Stockholm |
| ZIP/Postal code |
106 91 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE76514 |
Laser-capture microscopy coupled with Smart-seq2 (LCM-seq) for robust and efficient transcriptomic profiling of mouse and human tissues |
|
| Relations |
| BioSample |
SAMN04383884 |
| SRA |
SRX1516217 |
