|
| Status |
Public on Dec 06, 2020 |
| Title |
Hnrnpll_KO_G6_ESC |
| Sample type |
SRA |
| |
|
| Source name |
Hnrnpll KO EB-differentiation day 0
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic stem cell
genotype: Hnrnpll-/-
time: day 0
|
| Growth protocol |
ESC were culture in ES cell culture medium supplemented with 15% fetal bovine serum, 1000U/ml leukemia inhibitory factor. EBs were formed from ES cells by using handing drop culture method and collect the samples every other day.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols; illumina polyA+ RNA-seq library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Hnrnpll KO EB-differentiation day 0
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and low quality sequences with trimmomatics (version 0.36) with default parameters, then mapped to mm10 whole genome of GENCODE vM12 using hisat v2.0.5 with parameters --dta -t -p 8.
Both transcripts per kilobase of exon per million reads (TPM) and non-normalized raw counts were calculated using stringtie v1.3.3b with parameters -e -B -p 8.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM and non-normalized raw counts values for each sample.
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Jia Yu |
| E-mail(s) |
j-yu@ibms.pumc.edu.cn
|
| Organization name |
Peking Union Medical College
|
| Street address |
Dong Dan San Tiao 5, Dongcheng District
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE136955 |
Differential gene expression during embryoid body (EB) formation of mouse embryonic stem cells when Hnrnpll was depleted |
|
| Relations |
| BioSample |
SAMN12701974 |
| SRA |
SRX6808232 |
