|
| Status |
Public on Jun 19, 2019 |
| Title |
immortal.pod.pre-thermoswitch.r2 |
| Sample type |
SRA |
| |
|
| Source name |
immortalized podocyte culture
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: immortalized podocyte culture
heat shock activation: Cultured at 33C
|
| Treatment protocol |
cultured at 33C, which keeps the podocyte cell line proliferating. Protocols from PMID: 11856766 and 22591222.
|
| Growth protocol |
Saleem et al., 2002; Ni et al., 2012
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was exracted with Qiagen Rneasy micro kit (cat #: 74004)
Kapa stranded mRNA-Seq library (#KK8420)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
TT1805RNA16
RNASeq.pod_pre-shock.vs.pod_post-shock.xlsx
RNASeq.pod_pre-shock.vs.D28GFP+.xlsx
RNASeq.pod_pre-shock.vs.RC.xlsx
|
| Data processing |
Base call by bcl2fastq v. 2.17
Fastq files were aligned using TopHat2.
TPM values were calculated with Partek E/M distributed on Partekflow (http://www.partek.com/partek-flow/)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with TPM values
RNASeq.pod_pre-shock.vs.D28GFP+.xlsx: D28GFP+ samples refer to the D28GFP+ samples refers to those appears in GSE124392 (GSM3531625 -GSM3531628)
RNASeq.pod_post-shock.vs.D28GFP+.xlsx: D28GFP+ samples refer to the D28GFP+ samples refers to those appears in GSE124392 (GSM3531625 -GSM3531628)
RNASeq.pod_pre-shock.vs.RC.xlsx: RC samples refers to those appears in GSE127344 (GSM3634121- GSM3634124).
RNASeq.pod_post-shock.vs.RC.xlsx: RC samples refers to those appears in GSE127344 (GSM3634121- GSM3634124).
RNASeq.pod_pre-shock.vs.pod_post-shock.xlsx
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Jun 19, 2019 |
| Contact name |
Andrew P McMahon |
| E-mail(s) |
[email protected]
|
| Phone |
323-442-7847
|
| Organization name |
University of Southern California
|
| Department |
Stem Cell Biol & Regen Med
|
| Lab |
Andrew McMahon
|
| Street address |
1425 San Pablo St, BCC 312
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE127344 |
Transcriptomic profile of human embryonic renal corpuscles |
|
| Relations |
| BioSample |
SAMN11917829 |
| SRA |
SRX5944495 |
