|
| Status |
Public on Nov 24, 2014 |
| Title |
shRenilla in mir30 Replicate A |
| Sample type |
SRA |
| |
|
| Source name |
shRNA Infected HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
rna type: small RNAs
cell line: HEK293
|
| Treatment protocol |
Cells were infected at copy-number 1. Following infection cells were selected with G418 (1 mg/ml) until reaching 95% infection rate.
|
| Growth protocol |
ERC:DMEM supplemented with 10% FBS, 1 mM sodium pyruvate, 100 U/ml penicillin, and 100 μg/ml streptomycin
HEK293T: DMEM high glucose supplemented with 10% fetal bovine serum, non-essential amino acids and penicillin streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA < 200 bps was isolated using the mirVana miRNA isolation kit (Life Technologies). F
Following RNA isolation, smallRNAs were cloned using the illumina sRNA kit.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
size selected RNA
small RNAs from mir30 harbored shRenilla Infected cells
processed data file: Renilla_Variance_Stabalized.txt
|
| Data processing |
1) Gallus gallus and Homo sapiens microRNA fasta files were obtained from miRbase. Illumina adapter sequences were then appended to each guide sequence and the resultant files compiled using bowtie-build.
2) Fastq files were allinged to the index files described above with bowtie. Allowing two mismatches.
3) shRNA and microRNA counts were dtermined using uniq -c.
4) Counts were normalized using the DESeq getVarianceStabalizedData function.
5) Normalized shRNA counts were normalized further by their log2 fold change vs. the top 33% most expressed microRNAs.
Genome_build: galGal4 and hg19
Supplementary_files_format_and_content: Rpa3_Variance_Stabalized.txt & Renilla_Variance_Stabalized.txt, Each file has 5 fields: 1) shRNA/microRNA, 2) mir30-shRNA infected shRNA/microRNA normalized counts (replicate A), 3) mir30-shRNA infected shRNA/microRNA normalized counts (replicate B), 4) ultramiR-shRNA infected shRNA/microRNA normalized counts (replicate A), 5) ultramiR-shRNA infected shRNA/microRNA normalized counts (replicate B)
|
| |
|
| 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 |
GPL15520 |
| Series (2) |
| GSE62187 |
An optimized microRNA scaffold increases shRNA processing and target knockdown |
| GSE62189 |
A computational algorithm to predict shRNA potency |
|
| Relations |
| BioSample |
SAMN03100047 |
| SRA |
SRX729547 |
