|
| Status |
Public on Jul 30, 2019 |
| Title |
soma shPum2 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
cell bodies and axons of DRGs
|
| Organism |
Rattus norvegicus |
| Characteristics |
developmental stage: E15
cell type: somatic compartment of dorsal root ganglion neurons
shRNA: shPum2
|
| Treatment protocol |
Neurons were transduced with lentiviruses containing shControl or shPum2 on the day of plating.
|
| Growth protocol |
Rat embryonic dorsal root ganglion neurons were grown in microfluidic chambers for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the somatic and axonal compartments of microfluidic chambers using the Single Cell RNA Purification Kit from Norgen (Cat. 51800) as per manufacturer's instructions.
Libraries were prepared using standard or ultra-low input kits for somatic and axonal samples respectively (GENEWIZ, South Plainfield, NJ).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file: soma_shControl_vs_shPum2.txt
|
| Data processing |
Basecalls performed by HiSeq Control Software.
Sequenced reads were mapped to Rn6 using kallisto.
Mapped reads were analyzed for differential expression using DESeq2.
Genome_build: Rn6 (Rnor_6.0)
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include abundance counts from kallisto output.
Supplementary_files_format_and_content: *txt: Tab-delimited text files include differential expression from DESeq2 output, separately for axons and cell bodies.
|
| |
|
| Submission date |
Jul 29, 2019 |
| Last update date |
Aug 02, 2019 |
| Contact name |
Ulrich Hengst |
| E-mail(s) |
[email protected]
|
| Organization name |
Columbia University
|
| Department |
Pathology and Cell Biology
|
| Lab |
BB12-1210A
|
| Street address |
650 West 168th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE135073 |
Changes in axonal and somatic transcriptomes in response to Pum2 knockdown |
|
| Relations |
| BioSample |
SAMN12392733 |
| SRA |
SRX6612144 |
