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| Status |
Public on Dec 21, 2022 |
| Title |
Differential transcriptional responses to BIRC6 depletion between BIRC6-dependent and -nondependent cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To investigate the mechanism underlying the differing responses of cancer cells to BIRC6 depletion, we knocked out BIRC6 in a series of BIRC6-dependent and -nondependent cell lines. We subsequently profiled the effect of BIRC6 depletion on gene expression using RNA-sequencing.
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| Overall design |
Comparative gene expression profiling of three BIRC6-dependent (HCC202, SNU503, HCC95) and three BIRC6-nondependent (JIMT1, SW837, HCC15) cell lines that were transduced with an sgRNA against BIRC6 (sgBIRC6-1, -4; two different sgRNA sequences against BIRC6 were tested) or a control sgRNA (sgCh2-2). Two biological replicates were analyzed for each sample.
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| Contributor(s) |
Shibue T, Cervia LD, Vazquez F, Hahn WC |
| Citation(s) |
36576405 |
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| Submission date |
Dec 20, 2022 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Tsukasa Shibue |
| E-mail(s) |
tshibue@broadinstitute.org
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| Phone |
6177773407
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| Organization name |
Broad Institute of MIT and Harvard
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| Department |
Cancer Program
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| Lab |
DepMap TDA
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| Street address |
415 Main St., 4034-A
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (36)
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| GSM6865879 |
HCC202, sgBIRC6-1, rep 2 |
| GSM6865880 |
HCC202, sgBIRC6-4, rep 1 |
| GSM6865881 |
HCC202, sgBIRC6-4, rep 2 |
| GSM6865882 |
SNU503, sgCh2-2, rep 1 |
| GSM6865883 |
SNU503, sgCh2-2, rep 2 |
| GSM6865884 |
SNU503, sgBIRC6-1, rep 1 |
| GSM6865885 |
SNU503, sgBIRC6-1, rep 2 |
| GSM6865886 |
SNU503, sgBIRC6-4, rep 1 |
| GSM6865887 |
SNU503, sgBIRC6-4, rep 2 |
| GSM6865888 |
HCC95, sgCh2-2, rep 1 |
| GSM6865889 |
HCC95, sgCh2-2, rep 2 |
| GSM6865890 |
HCC95, sgBIRC6-1, rep 1 |
| GSM6865891 |
HCC95, sgBIRC6-1, rep 2 |
| GSM6865892 |
HCC95, sgBIRC6-4, rep 1 |
| GSM6865893 |
HCC95, sgBIRC6-4, rep 2 |
| GSM6865894 |
JIMT1, sgCh2-2, rep 1 |
| GSM6865895 |
JIMT1, sgCh2-2, rep 2 |
| GSM6865896 |
JIMT1, sgBIRC6-1, rep 1 |
| GSM6865897 |
JIMT1, sgBIRC6-1, rep 2 |
| GSM6865898 |
JIMT1, sgBIRC6-4, rep 1 |
| GSM6865899 |
JIMT1, sgBIRC6-4, rep 2 |
| GSM6865900 |
SW837, sgCh2-2, rep 1 |
| GSM6865901 |
SW837, sgCh2-2, rep 2 |
| GSM6865902 |
SW837, sgBIRC6-1, rep 1 |
| GSM6865903 |
SW837, sgBIRC6-1, rep 2 |
| GSM6865904 |
SW837, sgBIRC6-4, rep 1 |
| GSM6865905 |
SW837, sgBIRC6-4, rep 2 |
| GSM6865906 |
HCC15, sgCh2-2, rep 1 |
| GSM6865907 |
HCC15, sgCh2-2, rep 2 |
| GSM6865908 |
HCC15, sgBIRC6-1, rep 1 |
| GSM6865909 |
HCC15, sgBIRC6-1, rep 2 |
| GSM6865910 |
HCC15, sgBIRC6-4, rep 1 |
| GSM6865911 |
HCC15, sgBIRC6-4, rep 2 |
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| Relations |
| BioProject |
PRJNA914287 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE221430_BIRC6_DE_sgCh2-2_vs_sgBIRC6.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE221430_BIRC6_RNAseq.rsem_transcripts_tpm.txt.gz |
18.4 Mb |
(ftp)(http) |
TXT |
| GSE221430_BIRC6_rep_collapsed_logCPM.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE221430_RAW.tar |
183.6 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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