|
| Status |
Public on Oct 01, 2012 |
| Title |
shYAP (YAP knockdown) |
| Sample type |
SRA |
| |
|
| Source name |
shYAP (YAP knockdown)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mammary epithelial cell
passage: 3 to 4
cell line: MCF10A
|
| Growth protocol |
Stable MCF10A cell lines with YAP overexpression, YAP knockdown, or control vector were cultured in DMEM/F12 media supplemented with 5% horse serum, 20ng/mL EGF, 0.5ug/mL, 10ug/mL insulin, 100ng/mL cholera toxin, and 50ug/mL penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MicroRNA-enriched RNA was isolated from stable MCF10A cell lines using miRNeasy Mini Kit (Qiagen).
A small RNA library was generated from RNA samples according to Illumina's sample preparation instruction. Briefly, RNA sample was size fractionated, and 15-20 nt RNA was isolated and purified. Then 5' and 3' Adaptor ligation was done using T4 RNA ligase (Promega), then reverse transcribed, and PCR amplified, and the amplified product was purified for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
The purified cDNA library was used for cluster generation on Illumina's Cluster Station and then sequenced on Illumina GAIIx following vendor's instruction for running the instrument.
Raw sequencing reads were obtained using Illumina's Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module.
A proprieettary software package, ACGT101-miR v3.2 (LC Sciences) was used for standard data analysis
A series of digital filters (LC Sciences) were employed to remove various un-mappable reads.
Filtering by length. Default = 15 nt. For microRNA discovery.
Data further sorted by copy number.
Unique sequence mapped to mRNA was removed.
Genome_build: hg18
Supplementary_files_format_and_content: text files generated. Files include RAW data, Filtered Data, Mapped Data and the summary.
|
| |
|
| Submission date |
Sep 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Karen Tumaneng |
| Organization name |
UCSD-SCRM
|
| Street address |
2880 Torrey Pines Scenic Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE41124 |
YAP mediates crosstalk between the Hippo and PI3K-TOR pathway by suppressing PTEN via miR-29 |
|
| Relations |
| SRA |
SRX190410 |
| BioSample |
SAMN01737220 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1011898_Report_3582_shYAP.pdf.gz |
407.4 Kb |
(ftp)(http) |
PDF |
| GSM1011898_shYAP_Data_summary.xls.gz |
9.9 Kb |
(ftp)(http) |
XLS |
| GSM1011898_shYAP_FHG_clusterPosition.txt.gz |
43.6 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_db.fa.gz |
347.5 Kb |
(ftp)(http) |
FA |
| GSM1011898_shYAP_FHG_gp1_Align.txt.gz |
179.6 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp1_Sum.txt.gz |
22.8 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp1_miRlist.txt.gz |
103.5 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp2_Align.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp2_Sum.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp2_miRlist.txt.gz |
326 b |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp3_Align.txt.gz |
2.7 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp3_Sum.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp3_miRlist.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp4_Align.txt.gz |
70.9 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp4_Sum.txt.gz |
26.3 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_gp4_miRlist.txt.gz |
14.8 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_hc.txt.gz |
373.6 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_lc.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_long.txt.gz |
12.0 Mb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_miRdistribution.png.gz |
9.4 Kb |
(ftp)(http) |
PNG |
| GSM1011898_shYAP_FHG_nohit.txt.gz |
268.6 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_pass.txt.gz |
9.5 Mb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_short.txt.gz |
192.1 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_uni_miRs.txt.gz |
14.4 Kb |
(ftp)(http) |
TXT |
| GSM1011898_shYAP_FHG_unique.txt.gz |
19.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data are available on Series record |
