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Sample GSM4063638 Query DataSets for GSM4063638
Status Public on Dec 06, 2020
Title Hnrnpll_KO_H8_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 SAMN12701973
SRA SRX6808233

Supplementary file Size Download File type/resource
GSM4063638_Hnrnpll_KO_H8_ESC.TPM.txt.gz 457.0 Kb (ftp)(http) TXT
GSM4063638_Hnrnpll_KO_H8_ESC.counts.txt.gz 378.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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