|
| Status |
Public on Mar 29, 2018 |
| Title |
PolyA(+)_RNA-seq_DGCR8ko_EpiLC_48H |
| Sample type |
SRA |
| |
|
| Source name |
ESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell line: DGCR8 knockout ESC line
cell type: ESCs
culture condition: cultured in Differentiation medium for EpiLC induction for 48 hours
treatment: NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was extracted using Trizol reagent. TruSeq Stranded mRNA LT Sample Prep Kit (Cat# RS-122-2101) was used for polyA (+) RNA-seq sample preparation with 3 ug of total RNA. NBE Mutiple small RNA librariry prep set (Cat# E7580S) was used for small RNA-seq sample preparation.
RNA libraries for polyA(+) RNA-seq and small RNA-seq were prepared following the manufacturer's protocols, respectively
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
DGCR8 knock-out
EpiLC_differentiation.txt
PolyA_+_RNA-seq_DGCR8ko_EpiLC_48H
|
| Data processing |
Bowtie software was used to align sequencing reads to reference mRNA and miRNA database
For polyA(+) RNA-seq, mouse cDNA database (Ensembl, GRCm38) was use for alignment
For small RNA-seq, homemade PERL software was used to remove adaptor sequences, and 20-25nt small RNAs was aligned to known mature miRNA sequences (miRBase)
both polyA(+) and small RNA-seq, Reads per Million was culculated for the normaliztion
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample
|
| |
|
| Submission date |
Mar 26, 2018 |
| Last update date |
Mar 29, 2018 |
| Contact name |
Peng Du |
| E-mail(s) |
Peng.Du@childrens.harvard.edu
|
| Organization name |
Boston Children’s Hospital, Harvard Medical School
|
| Lab |
Richard Gregory
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE112334 |
An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition |
|
| Relations |
| BioSample |
SAMN08796045 |
| SRA |
SRX3848050 |
