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Status |
Public on Jul 13, 2018 |
Title |
eIF1A KD1 [Mars-seq] |
Sample type |
SRA |
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Source name |
Mouse embryonic fibroblasts
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Organism |
Mus musculus |
Characteristics |
cell type: fibroblasts passage: passages 5-8 treatment: Si-eIF1A (X+18) transfection
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Treatment protocol |
Si-RNA [Si-Negative control or Si-eIF1A (X+18)] tranfection was performed using Lipofectamine RNAimax
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Growth protocol |
MEFs were grown in standard growth condition in 10 cm plates
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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)
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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 |
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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 |
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Relations |
BioSample |
SAMN09645071 |
SRA |
SRX4383846 |