|
| Status |
Public on Sep 10, 2018 |
| Title |
HSF1i.37.3 |
| Sample type |
SRA |
| |
|
| Source name |
Madin Darby canine kidney (MDCK) cells transduced with inducible inhibitor of HSF1, HSF1i.37
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell line: MDCK
transduction: inducible inhibitor of HSF1
treatment: 1 ug/ml Doxycycline in water for 48 hours at 37 degrees C
|
| Treatment protocol |
1 ug/ml tetracycline in water for 48 hr or 0.1% DMSO for 48hr each group at 37 °C or 39 °C
|
| Growth protocol |
MDCK cells expressing doxycycline-inducible dn-cHSF1 construct were cultured at 37 °C or 39 °C in a 5% CO2 atmosphere in DMEM (CellGro) supplemented with 10% fetal bovine serum (CellGro) and 1% penicillin/streptomycin/glutamine (CellGro).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cellular RNA was harvested using the Qiagen RNeasy Plus Mini Kit with QIAshredder homogenization columns.
Kapa mRNA HyperPrep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
annapon_counts.txt
annapon_l2tpm.txt
d1100
|
| Data processing |
HiSeq2000 using v3 chemistry. Software: Control software version 2.0.12.0, RTA version 1.17.21.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequence aligned and transcripts quantified using star2.5.3a, rsem1.3.0 and samtools 1.3
Genome_build: canFam3 with ENSEMBL annotation
Supplementary_files_format_and_content: annapon_counts.txt is parsed integer counts for samples from rsem
Supplementary_files_format_and_content: annapon_l2tpm.txt is parsed tpm for samples from rsem transformed to log2 space by adding 1 to TPM and calculating the log2 value
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Sep 10, 2018 |
| Contact name |
Charles Arthur Whittaker |
| E-mail(s) |
charliew@mit.edu
|
| Organization name |
Koch Institute
|
| Street address |
77 Mass Ave 76-189
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02152 |
| Country |
USA |
| |
|
| Platform ID |
GPL16540 |
| Series (1) |
| GSE113649 |
Host chaperones can define the fitness of adaptive influenza variants |
|
| Relations |
| BioSample |
SAMN08981293 |
| SRA |
SRX3993907 |
