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Sample GSM7703363 Query DataSets for GSM7703363
Status Public on Sep 16, 2024
Title KAP1-KCL-30min-REP1
Sample type SRA
 
Source name primary mouse neuronal cells
Organism Mus musculus
Characteristics antibody: KAP1(Abcam, ab22553)
cell line: primary mouse neuronal cells
cell type: mouse neuronal
treatment: KCL-30min
Treatment protocol 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.
Growth protocol MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.
Extracted molecule genomic DNA
Extraction protocol CUT&Tag standard Protocol
PCR Ampfication
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing cutadapt: -u 15 -U 15 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -b -B
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2: -q --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
makeUCSCfile
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: BedGraph
Library strategy: CUT&Tag
 
Submission date Aug 10, 2023
Last update date Sep 16, 2024
Contact name Lishuan Wang
E-mail(s) weiyuan1220@gmail.com
Phone 6262054087
Organization name UCSD
Lab Rosenfeld, Michael
Street address 9500 Gilman Drive
City SAN DIEGO
State/province California
ZIP/Postal code 92093
Country USA
 
Platform ID GPL24247
Series (2)
GSE240599 An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs
GSE240603 An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs
Relations
BioSample SAMN36938654
SRA SRX21331783

Supplementary file Size Download File type/resource
GSM7703363_KAP1-KCL-30min-REP1.bw 45.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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