|
| Status |
Public on May 01, 2024 |
| Title |
ATAC-Seq, shBRD9-81-A |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell type: CD34 HSPC
genotype: BRD9 knockdown
treatment: Lentiviral infection/FACS sort
|
| Treatment protocol |
High titer lentivirus infection was carried out at MOI 30 in presence of 10 microg/mL protamine sulphate
|
| Growth protocol |
Cells were placed in CD34 media containing IMDM+20%BIT and 100ng/mL rH-SCF and FL, and 50ng/mL TPO, supplemented with 100microM 2-mercaptoethanol and genatmicin/ciprofloxacin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
nuclei were treated with Tn5 enzyme
Tagmented DNA was barcoded with Nextera Index kit v2
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
shBRD9 rep A
KD12.merged_peaks.bed.gz
|
| Data processing |
Sequence reads were trimmed for adapter sequences and poor quality nucleotides using Trimmomatic v.0.38
Trimmed reads were aligned to reference genome hg38 using bowtie2
Samtools 1.9 was used to filter aligned reads
Picard 2.18.26 was used to remove optical duplicates, mtDNA and unplaced contigs were removed prior to peak calling
MACS2 2.1.2 was used for peak calling. Valid peaks from each group or condition were then merged and peaks called in at least 66% of samples were kept for downstream analyses
Assembly: hg38
Supplementary files format and content: bed files merged peaks
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Swati Garg |
| E-mail(s) |
swati.garg15@gmail.com
|
| Organization name |
Dana Farber Cancer Institute
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE264030 |
BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN40975814 |
| SRA |
SRX24282631 |
