|
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
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|
|
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 |