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Sample GSM3266824 Query DataSets for GSM3266824
Status Public on Jul 13, 2018
Title eIF1A KD1 [Mars-seq]
Sample type SRA
 
Source name Mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: fibroblasts
passage: passages 5-8
treatment: Si-eIF1A (X+18) transfection
Treatment protocol Si-RNA [Si-Negative control or Si-eIF1A (X+18)] tranfection was performed using Lipofectamine RNAimax
Growth protocol MEFs were grown in standard growth condition in 10 cm plates
Extracted molecule total RNA
Extraction protocol Cell lysates were thawed and messanger RNA was captured with 15ul of NEB oligo(dT) beads, and washed according to manufacture guidelines.
Purified messanger RNA was eluted at 70C with 60ul of 10mM Tris-Cl pH 7.5 and stored at -80C.For library preparation RNA was used for the bulk MARS-seq protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 -q 20 -m 30 )
The remaining reads (raw data submitted) were mapped to mm10 (igenomes) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts <=5 . Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: contains normalized DESeq2 counts (not UMI counts)
 
Submission date Jul 12, 2018
Last update date Jul 13, 2018
Contact name Dena Leshkowitz
E-mail(s) dena.leshkowitz@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Bioinformatics Unit, Life Sciences Core Facilities
Street address P.O.B. 26
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL19057
Series (2)
GSE116982 Cancer associated mutants of eIF1A impair Rps3/Rps10 binding and enhance scanning of cell cycle genes [Mars-seq]
GSE116983 Cancer associated mutants of eIF1A impair Rps3/Rps10 binding and enhance scanning of cell cycle genes
Relations
BioSample SAMN09645071
SRA SRX4383846

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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