NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7876341 Query DataSets for GSM7876341
Status Public on Jul 17, 2024
Title primary cortical neurons, H2BE-KO
Sample type SRA
 
Source name primary cortical neurons
Organism Mus musculus
Characteristics age: E16.5
cell type: primary cortical neurons
genotype: H2BE-KO/mCherry-KI
Extracted molecule genomic DNA
Extraction protocol At 12DIV, primary cortical neurons were collected in wash buffer (Kaya-Okur et al. 2019) and CUT&Tag was performed with anti-H2BE antibody (Millipore ABE1384)
Transposition reaction mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer)
Nextera primer sets with NEBNext Master Mix was used to generate libraries with AMPure beads used for cleanup
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Data processing Fastq files were aligned by Bowtie2
bam files were generated using SAMtools
NGSplot was used to generate metaplots
tdf files were generated using IGVtools
Assembly: mm10
Supplementary files format and content: tdf files generated by IGVtools from bam files aligned to bowtie2
Library strategy: CUT&TAG
 
Submission date Nov 01, 2023
Last update date Jul 17, 2024
Contact name Emily Feierman
E-mail(s) emily.feierman@gmail.com
Organization name University of Pennsylvania
Street address 3400 Civic Center Blvd
City Philadelphia
ZIP/Postal code 19104
Country USA
 
Platform ID GPL21626
Series (2)
GSE246688 CUT&Tag, ATAC-seq, bulk RNA-seq and single-nucleus RNA-seq analysis of histone variant H2BE in cortical neurons
GSE246748 CUT&Tag seq analysis of histone variant H2BE in neurons [H2BE_CT_antibodyValidation]
Relations
BioSample SAMN38060212
SRA SRX22328038

Supplementary file Size Download File type/resource
GSM7876341_ERF-KO-H2BE-030422_S18_ME_R1_001.uniqmapped_rmdup.tdf 102.7 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.