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Sample GSM3181736 Query DataSets for GSM3181736
Status Public on Oct 26, 2018
Title WT E14 HS RNA replicate2
Sample type SRA
 
Source name Mouse hindstomach epithelial cells
Organism Mus musculus
Characteristics strain: CD1 wild type
cell type: Embryonic epithelial cells from the hindstomach
genotype: Wild-Type
developmental stage: E14
Treatment protocol No treatment
Extracted molecule total RNA
Extraction protocol E14 hindstomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description E14 HS_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt
Data processing Alignment: ATAC-seq and ChIP-seq: Bowtie2. RNA-seq: STAR aligner, version 2.5.3a.
ATAC-seq differential region identification: diffReps; Peak calling: MACS2; RNA-seq raw read counts: HTSeq
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: ATAC-Seq & ChIP-seq: bigwig file for visualizing aligned sequence tags (available in tar archives on the series record).
Supplementary_files_format_and_content: RNA-seq: text file with raw read counts
 
Submission date Jun 08, 2018
Last update date Oct 26, 2018
Contact name Ramesh Shivdasani
E-mail(s) ramesh_shivdasani@dfci.harvard.edu
Organization name Dana Farber Cancer Institute
Department Medical Oncology
Lab Shivdasani
Street address 450 Brookline Ave. Dana 720D
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL19057
Series (1)
GSE115541 Chromatin and tissue plasticity precede commitment to intestinal differentiation during endoderm development
Relations
BioSample SAMN09385801
SRA SRX4187789

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

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