|
| Status |
Public on Sep 16, 2017 |
| Title |
293T pTIP-scr 100hrs (duplicate 1) |
| Sample type |
SRA |
| |
|
| Source name |
ATCC CRL-3216
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T (pool of 3 KO clones)
tissue: Human Embryonic kidney
infection: Infected with pTIP-scr; 100ng/uL doxycycline
time point: harvested at 100hrs
genotype: Fas ligand KO -/-
|
| Treatment protocol |
HeyA8 ΔshR6 clone #11 was infected with pLKO-shScr or pLKO-shR6. A pool of three 293T ΔshL3 clones was infected with either pTIP-shScr or pTIP-shL3. After selection with puromycin, the pTIP-infected 293T cells were plated with Doxycycline (100ng/uL) in duplicate at 500,000 cells per T175 flask. The pLKO-infected HeyA8 cells were plated in duplicate at 500,000 cells per flask. Total RNA was harvested 50 hours and 100 hours after plating.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol. Two small RNA-SEQ sub-libraries were generated: one containing library fragments 140-150 bp in size and one containing library fragments 150-200 bp in size (both including the sequencing adator of about 130bp).
sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
chr1:172,665,726-172,665,766 deletion
293T_shSCR_100hr_rep1_sm
|
| Data processing |
Sequenced reads were mapped to hg38 human genome using Tophat and bowtie2
raw counts were calculated by HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with log2FoldChange values, p-values and adjusted p-values.
|
| |
|
| Submission date |
Jul 11, 2017 |
| Last update date |
Sep 08, 2022 |
| Contact name |
Marcus Peter |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Street address |
303 East Superior Street, Lurie 6-123
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE87817 |
CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes |
| GSE101183 |
CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [shL3.shR6.RNAseq.sm] |
|
| Relations |
| BioSample |
SAMN07342513 |
| SRA |
SRX2995941 |
