|
| Status |
Public on Aug 23, 2018 |
| Title |
RNA sequencing of lncRNAs knockdown in human pancreatic cancer cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We report the transcriptome changes that result from the transient knockdown of FAM83H-AS1 in Aspc1 cells and transient knockdown of LINC00673 in Panc1 cells.
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| |
|
| Overall design |
Total RNA extracted 48 hour after transfection with targeting and control siRNAs. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2500 (Illumina) instrument. Reads were mapped to the human genome (UCSC/hg19) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DESeq2.
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| |
|
| Contributor(s) |
Arnes L, Liu Z, Olive KP, Rabadan R, Wang J |
| Citation(s) |
29440233 |
| |
| Submission date |
Mar 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Luis Arnes |
| E-mail(s) |
la2384@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Biomedical Informatics
|
| Street address |
1130 St Nicholas avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (15)
|
|
| Relations |
| BioProject |
PRJNA380131 |
| SRA |
SRP102315 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE96931_DEseq_LA001-LA002-LA003-LA004_DEG_list.csv.gz |
927.6 Kb |
(ftp)(http) |
CSV |
| GSE96931_DEseq_LA001-LA002-LA005-LA006_DEG_list.csv.gz |
943.7 Kb |
(ftp)(http) |
CSV |
| GSE96931_DEseq_LD001-LD002-LD009_LD005-LD006-LD010_DEG_list.xlsx |
4.4 Mb |
(ftp)(http) |
XLSX |
| GSE96931_DEseq_LD001-LD002-LD009_LD007-LD008-LD011_DEG_list.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE96931_RAW.tar |
13.5 Mb |
(http)(custom) |
TAR (of CSV) |
| GSE96931_Sup_table_1_PDA-lncRNAs.xlsx |
338.3 Kb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_2_molecular_subtyping.xlsx |
59.3 Kb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_3_DE_list_Non_coding_clusters.xlsx |
9.5 Mb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_4_LCM_raw-counts.xlsx |
252.4 Kb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_5_FAM83H-AS1.xlsx |
421.5 Kb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_6_TCGA_Network.xlsx |
11.1 Mb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_7_LINC00673.xlsx |
1.1 Mb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_8_SOX9.xlsx |
26.3 Kb |
(ftp)(http) |
XLSX |
| GSE96931_Sup_table_9_m_m.xlsx |
11.0 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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