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Sample GSM1521518 Query DataSets for GSM1521518
Status Public on Nov 24, 2014
Title shRPA3 in mir30 Replicate A
Sample type SRA
 
Source name shRNA Infected ERC cells
Organism Gallus gallus
Characteristics rna type: small RNAs
cell line: ERC
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 shRPA3 Infected cells
processed data file: Rpa3_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 GPL19064
Series (2)
GSE62187 An optimized microRNA scaffold increases shRNA processing and target knockdown
GSE62189 A computational algorithm to predict shRNA potency
Relations
BioSample SAMN03100043
SRA SRX729543

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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