|
| Status |
Public on May 01, 2024 |
| Title |
Replicate F GFP-Low 15K lib transduced |
| Sample type |
SRA |
| |
|
| Source name |
HUDEP-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP-2
cell type: human erythroid progenitors
genotype: WT
treatment: untreated
|
| Growth protocol |
HUDEP-2 were maintained in Iscove's modified Dulbecco's medium (IMDM) supplemented with 330 μg/mL human holo-transferrin (Sigma), 10 μg/mL recombinant human insulin (Sigma), 2 IU/mL heparin (Sigma), 5% human AB plasma (obtained from Bloodworks Northwest, Seattle, WA), 3 IU/mL EPO, 100 ng/mL SCF, 1 μg/mL doxycycline (Sigma), and 100 units/ml penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA from enhancer screening library transduced HUDEP-2 cells was isolated using the DNeasy Blood & Tissue kit (Qiagen, 69504)
PCR amplicons indexed with Nextera dual indexes
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Cloning region flanking sequences were trimmed using seqtk (https://github.com/lh3/seqtk) using the trimfq command and removing 22 bases from read1 and 20 from read2
Illumina adapters were trimmed using Trimmomatic v0.36 setting the ILLUMINACLIP argument to 2:30:10:2:true
Sequences were aligned against the GRCh38 reference genome with BWA and sequences were filtered using samtools with the following arguments: view -q 1 -f 64.
Sequences were converted to genomic coordinates BED file using the bam2bed tool from the BEDOPS suite
For every reference sequence (tile or full DHS depending on screening vector library) we counted the number of reads in each sample that overlap the reference sequence by ≥90% using the bedmap tool from BEDOPS.
Assembly: GRCh38
Supplementary files format and content: gzipped tab delimited table containing raw counts per tile across samples
Library strategy: DNAseq
|
| |
|
| Submission date |
Dec 27, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Jeff Vierstra |
| E-mail(s) |
jvierstra@altius.org
|
| Organization name |
Altius Institute for Biomedical Sciences
|
| Street address |
2211 Elliot Ave
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98121 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE252159 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [DNAseq] |
| GSE252163 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors |
|
| Relations |
| BioSample |
SAMN39152154 |
| SRA |
SRX23045013 |
