|
| Status |
Public on Jun 25, 2020 |
| Title |
Parental cell line (replicate 1) RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: undifferentiated ES cells
Sex: female
strain: C57BL/6J x CAST/EiJ hybrid
genotype/variation: wild type
|
| Growth protocol |
Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol extraction, rRNA was depleted and RNA fragmented by heating in presence of Mg2+, CDNA 1st strand was produced using random primers
NEBNext Ultra Directional RNA Second Strand Synthesis Module (E7550S) was used as described with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (E6240L) for multiplexed library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNAseq-WT.c.bw
RNAseq-WT.w.bw
|
| Data processing |
Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using TopHat2 (Kim et al., 2013)
Mapped reads were further analyzed by Homer(ver 4.8) (Heinz et al., 2010) to generate a raw read count table
DESeq2 package (Love et al. 2014) was used for downstream RNA-seq analysis
Strand-specific coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (w:watson, c:crick strand) and fpm normalized
|
| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Eric Aeby |
| E-mail(s) |
aeby@molbio.mgh.harvard.edu
|
| Organization name |
Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School
|
| Department |
Department of Molecular Biology and Department of Genetics
|
| Lab |
Lee Lab
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE118919 |
Transcriptome-wide analysis upon DCP1A knockout |
| GSE118943 |
DCP1A knockout: transcriptome-wide characterization |
|
| Relations |
| BioSample |
SAMN09881729 |
| SRA |
SRX4597441 |
