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| Status |
Public on May 07, 2024 |
| Title |
HEK293T_DTAG_ATAC-seq rep6 |
| Sample type |
SRA |
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| Source name |
HEK_CloneZD29
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK_CloneZD29
genotype: ZNF143 tagged with an inducible degron tag
treatment: 50nm dTAGV-1 treatment
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| Treatment protocol |
HEK-293T cells were collected after either no treatment or after 30 minutes of 50nm dTAGV-1 treatment
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
At the time of harvest, cells were moved to ice and scraped in 1mL ice cold PBS, and 100μL (∼5 x 10^4 cells) were transferred to 1.5 mL tubes. Cells were centrifuged at 500 x g for 5 minutes at 4°C, and the pellets were resuspended in 50 μL cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, adjusted to pH 7.4) and incubated on ice for 3 minutes. Samples were washed with 1 mL cold wash buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20). Cells were centrifuged at 500 x g for 10 minutes at 4°C, and pellets were resuspended in the transposition reaction mix (25 μL 2X TD buffer (Illumina), 2.5 μL TDE1 Tn5 transposase (Illumina), 16.5 μL PBS, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 5 μL nuclease-free water) and incubated in a thermomixer at 37°C and 100rpm for 30 minutes. DNA was extracted with the DNA Clean and Concentrator-5 Kit (Zymo Research).
Sequencing adapters were attached to the transposed DNA fragments using NEBNext Ultra II Q5 PCR mix (New England Biolabs), and libraries were amplified with 8 cycles of PCR. PEG-mediated size fractionation (Lis 1980) was performed on the libraries by mixing SPRIs-elect beads (Beckman) with each sample at a 0.5:1 ratio, then placing the reaction vessels on a magnetic stand. The right side selected sample was transferred to a new reaction vessel, and more beads were added for a final ratio of 1.8:1. The final size-selected sample was eluted into nuclease-free water. This size selection protocol was repeated to further remove large fragments.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
ZNF143_degron_ATAC_summits.bed
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| Data processing |
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication:https://github.com/guertinlab/fqdedupv1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation:https://github.com/guertinlab/seqOutBiasv1.3.1
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: peak summit counts files
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| Submission date |
May 02, 2024 |
| Last update date |
May 07, 2024 |
| Contact name |
Jinhong Dong |
| E-mail(s) |
jdong@uchc.edu
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| Organization name |
University of Connecticut
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| Department |
Center for Cell Analysis and Modeling
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| Street address |
400 Farmington Ave
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE266490 |
ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes (ATAC-seq) |
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| Relations |
| BioSample |
SAMN41178852 |
| SRA |
SRX24438458 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8248127_HEK293T_DTAG_rep6.hg38.bigWig |
79.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
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