|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Oct 28, 2016 |
Title |
Snhg3-PromoterDeletion-150126-F7 |
Sample type |
SRA |
|
|
Source name |
F1 2-1 129/Castaneus Female mESCs
|
Organism |
Mus musculus |
Characteristics |
cell type: embryonic stem cell cell line: Snhg3-PromoterDeletion-150126-F7 gender: female
|
Growth protocol |
Male ES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows: 1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).
|
Extracted molecule |
polyA RNA |
Extraction protocol |
p(A)+ RNA-seq with hybrid selection: We generated RNA sequencing libraries as described in Engreitz et al. Cell 2014. We performed hybrid selection after barcoding of DNA libraries on a combined pool as described in Gnirke et al. Nature Biotech 2009. ATAC-Seq: We performed ATAC-Seq as previously described (Buenrostro JD et al. Nature Methods 2013) using 50,000 mESCs. PRO-Seq: We performed PRO-Seq essentially as described in Kwak H et al. Science 2013. ChIP-Seq: We performed ChIP-Seq as described in Busby M et al. biorXiv 2016.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
poly(A)+ RNA-seq with hybrid selection
|
Data processing |
DNA sequencing (ATAC-Seq) and RNA sequencing (PRO-Seq and RNA-seq) analyses were performed as previously described (Engreitz et al. Cell 2014) except that data were initially aligned to both the 129S1 and Castanets genomes and reads were merged using pysuspenders. For RNA-seq experiments, reads mapping to specifically to the 129 or Castaneus alleles were counted for each gene (including any read overlapping an intron or exon) Genome_build: mm9 Supplementary_files_format_and_content: TDF: Coverage at 5bp resolution across genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/) Supplementary_files_format_and_content: BED: Read counts mapping specifically to the 129 or Castaneus alleles. Columns: chromosome, start, end, gene, count-129, count-castaneus
|
|
|
Submission date |
Aug 18, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Jesse Engreitz |
Organization name |
Stanford University
|
Street address |
240 Pasteur Drive
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE85798 |
Local regulation of gene expression by lncRNA promoters, transcription, and splicing |
|
Relations |
BioSample |
SAMN05590799 |
SRA |
SRX2032798 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2284491_Snhg3-PromoterDeletion-150126-F7.CountReads.bed.gz |
11.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|