|
Status |
Public on Nov 24, 2014 |
Title |
shRenilla in ultramiR 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 ultramiR 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 |
SAMN03100049 |
SRA |
SRX729549 |