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Sample GSM4072000 Query DataSets for GSM4072000
Status Public on Sep 10, 2024
Title Input_IM15KO_rep2
Sample type SRA
 
Source name Mouse islets
Organism Mus musculus
Characteristics passage/age: 8 weeks
strain: C57BL/6
Growth protocol MIN6
Extracted molecule genomic DNA
Extraction protocol Johnson et al., 2007, Science 316: 1497- 1502
SMARTer® ThruPLEX® DNA-Seq Kit
Paired end (MIN6) and single reads (islets)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Input
Illumina NextSeq500
Data processing ChIP-seq reads were aligned to the mm10 genome assembly using BWA and filtered for PCR duplicates.
For MIN6 cells, treatment samples were called using input as control with a q value of 0.05 in MACS2v2.2.1. For islets, EaSeq v1.111 "find peak" function was used with adaptive threshold function for control versus knockout islets (Med15) and control versus input (Med1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
 
Submission date Sep 09, 2019
Last update date Sep 10, 2024
Contact name Francis C Lynn
E-mail(s) fclynn@interchange.ubc.ca
Phone 6048752000
Organization name University of British Columbia
Department Surgery
Lab Lynn
Street address 950 28th Ave W
City Vancouver
State/province BC
ZIP/Postal code V5Z 4H4
Country Canada
 
Platform ID GPL19057
Series (1)
GSE137145 Transcriptional coactivator MED15 is required for beta cell maturation
Relations
BioSample SAMN12718752
SRA SRX6821920

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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