|
Status |
Public on Sep 16, 2024 |
Title |
CREB1-KCL-1h-REP1 |
Sample type |
SRA |
|
|
Source name |
primary mouse neuronal cells
|
Organism |
Mus musculus |
Characteristics |
antibody: CREB1(Milloipore, 17-600) cell line: primary mouse neuronal cells cell type: mouse neuronal treatment: KCL-1h
|
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 |
SAMN36938656 |
SRA |
SRX21331781 |