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| Status |
Public on Apr 01, 2023 |
| Title |
MIG-EV, rep 3 |
| Sample type |
SRA |
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| Source name |
Hematopoietic progenitor cells
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| Organism |
Mus musculus |
| Characteristics |
parental cell line: HPC7
cell line: MIG-EV, rep 3-HPC7
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| Growth protocol |
HPC7 cells were maintained in IMDM supplemented with 10% fetal bovine serum (Sigma), penicillin (100 U/ml), streptomycin (100 µg/ml), 2 mM L-glutamine (Gibco), 0.05 mM 2-mercaptoethanol and 100 µg/ml mSCF (Peprotech).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
100,000 cells were collected and washed with PBS and pelleted by centrifugation (300 g). Cells were then washed with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) following a 3 min incubation on ice.
The tagmentation reaction was performed in a thermocycler for 30 mins at 37°C with 1x TD buffer, 0.3x PBS, 0.1% Tween 20, 2.5 µl Tn5 (Illumina) in a 50 µl volume as previously described (Corces et al. 2017).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
HPC7 cells transduced with an empty retroviral vector as a transduction control
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| Data processing |
Reads were filtered with FASTP (Chen et. al., 2018) using the parameters - fastp -l 35 -W 3 -5 -3
Singleton reads were discarded (fastq-pair)
Paired-end reads were aligned using Bowtie2 (Langmead and Salzberg, 2012) to the reference genome (mm10)
Aligned reads were filtered for optical and PCR duplicates (Picard Tools)
Reads aligning to ENCODE blacklisted regions (Amemiya et. al., 2019), mitochondrial genome, improper pairs, and mapping quality <20 were discarded
Analysis of differential enrichment at promoter regions (-1kb to 100bp around the TSS) was performed using DiffBind (Stark et al 2011)
Genome_build: Illumina iGenomes UCSC reference genome (mm10) & gene annotation
Supplementary_files_format_and_content: CSV file was generated from DiffBind (Bioconductor R) and contains results of differential enrichment analysis at gene promoters
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| Submission date |
Apr 01, 2020 |
| Last update date |
Apr 01, 2023 |
| Contact name |
Kevin Robert Gillinder |
| Organization name |
Monash University
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| Department |
Australian Centre for Blood Diseases
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| Street address |
99 Commercial Road
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| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3004 |
| Country |
Australia |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE147873 |
Overexpression of the EMT modulator SNAI1 in HPC7 cells |
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| Relations |
| BioSample |
SAMN14517205 |
| SRA |
SRX8041921 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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