|
| Status |
Public on Nov 24, 2014 |
| Title |
shRNA Slpi1U1 Replicate A_1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse 4T1 Cell Line
|
| Organism |
Mus musculus |
| Characteristics |
cell treatment: shRNA Infected Cells
cell line: 4T1
|
| Treatment protocol |
Cells were infected at 0,3 MOI and selected to >95% infection percentage (averge of 10 days). shRNA-66708 abd 88943 infected cells were selexted with 1 μg/ml Puromycin . All other shRNA infected cells were selected with 500 μg/ml hygromycin.
|
| Growth protocol |
DMEM high glucose (Life Technologies) supplemented with 5% fetal bovine serum (Thermo Scientific), 5% fetal calf serum (Thermo Scientific), non-essential amino acids (Life Technologies) and penicillin streptomycin (Life Technologies)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified and DNAse treated using the Qiagen RNeasy Mini Kit
The NuGEN Ovation RNA-Seq V2 protocol was carried out on 100 ng of total RNA. cDNA was fragmented using the Covaris LE220 sonicator according to the manufacturer’s instruction to yield a target fragment size of 200 bp. The fragmented cDNA was subsequently processed using the NuGEN Ovation Ultralow DR Multiplex System. Libraries were analyzed on an Illumina Hiseq 2 using 76bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: Slpi.variance_stabalized
|
| Data processing |
1) Reads were alligned to the mm10 genome using bowtie-2.
2) Each gene's read counts were determined using htseq -count (python) function.
3) Reads were normalized across samples using DESeq (bioconductor)
mgp_variance_stabalized.txt and mgp_stabalized.txt each have 11 fields.
mgp_variance_stabalized
1) Gene Name
2) Normalized Counts for cells infected with 88943 (replicate A)
3) Normalized Counts for cells infected with 88943 (replicate B)
4) Normalized Counts for cells infected with Mgp1 (replicate A)
5) Normalized Counts for cells infected with Mgp1 (replicate B)
6) Normalized Counts for cells infected with Mgp1U1 (replicate A)
7) Normalized Counts for cells infected with Mgp1U1 (replicate B)
8) Normalized Counts for cells infected with Mgp1U3 (replicate A)
9) Normalized Counts for cells infected with Mgp1U3 (replicate B)
10) Normalized Counts for cells infected with Mgp2 (replicate A)
11) Normalized Counts for cells infected with Mgp2 (replicate B)
slpi_variance_stabalized
1) Gene Name
2) Normalized Counts for cells infected with 66708 (replicate A)
3) Normalized Counts for cells infected with 66708 (replicate B)
4) Normalized Counts for cells infected with Slpi1U1 (replicate A)
5) Normalized Counts for cells infected with Slpi1U1 (replicate B)
6) Normalized Counts for cells infected with Slpi1U2 (replicate A)
7) Normalized Counts for cells infected with Slpi1U2 (replicate B)
8) Normalized Counts for cells infected with Slpi2 (replicate A)
9) Normalized Counts for cells infected with Slpi2 (replicate B)
10) Normalized Counts for cells infected with Slpi4 (replicate A)
11) Normalized Counts for cells infected with Slpi4 (replicate B)
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts for cells infected with indicated shRNA.
|
| |
|
| Submission date |
Oct 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Simon Robert Vincent Knott |
| Organization name |
Cold Spring Harbor Laboratory
|
| Department |
Biology
|
| Lab |
Hannon
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE62184 |
shRNA off target analysis via RNAseq |
| GSE62189 |
A computational algorithm to predict shRNA potency |
|
| Relations |
| BioSample |
SAMN03100052 |
| SRA |
SRX729491 |
