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Sample GSM4809410 Query DataSets for GSM4809410
Status Public on Sep 29, 2020
Title QKO_ES_shBcat_2i_48hr_rep2
Sample type SRA
 
Source name QKO_ES_shBcat_2i_48hr_rep2
Organism Mus musculus
Characteristics cell type: embryonic stem cell
culture condition: 2i
Treatment protocol Beta-catenin knowndown in ES cell and epiLC
Growth protocol 2i media
Extracted molecule total RNA
Extraction protocol RNA was isolated by first homogenizing cells in 1ml TRIzol reagent (Invitrogen 15596026) through triturating the cell lysate through a 27-gauge needle a minimum of 7 times. Homogenized samples were mixed with 200µ l chloroform and vigorously shaken by hand for 30sec. Samples were then incubated at RT for 10min before centrifuging at 12,000g for 10min at RT. The aqueous phase containing RNA was transferred to a new tube, mixed with 100µ l chloroform, and subjected to a second round of shaking, incubation and centrifuging. The aqueous phase was transferred to a new tube containing 1.5µ l 20mg/ml glycogen, and mixed with 450µ l isopropanol to pre- cipitate RNA. Samples were gently mixed and incubated at RT for 10min before centrifuging at 4 °C for 15min. The supernatant was discarded and the pellet was washed by 1ml 75% ethanol. After the wash the RNA pellet was dried at RT for 20min and resuspended in RNase-free water. Yield and purity of RNA was determined by spectrophotometry with Nano drop (Thermo Scien- tific). The RNA was treated with DNase (Promega M6101)
RNA-seq and ChIP-seq libraries were prepared using the TruSeq RNA kit for sequencing,
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Trizol extraction
RSEM_TPM_table_2742.csv
Data processing Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome mm10 from UCSC using STAR aligner
TPM expression was generated using RSEM
ChIP-seq was aligned to genome mm10 using bowtie2
Bigwig files are normalized and extended to fragment length for IP samples
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq TPM in excel file, ChIP-seq in bigwig files
 
Submission date Sep 29, 2020
Last update date Oct 01, 2020
Contact name Shiyuan (Cynthia) Chen
E-mail(s) shc@stowers.org
Organization name Stowers Institute for Medical Research
Department Computational Biology
Street address 1000 E 50th St
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL19057
Series (1)
GSE108620 β-catenin associated protein complex maintains ground state mouse embryonic stem cell by regulating lineage development
Relations
BioSample SAMN16289275
SRA SRX9213055

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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