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| Status |
Public on Sep 10, 2020 |
| Title |
B(HT-4) |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Gallus gallus |
| Characteristics |
treatment type: high temperature
tissue: liver
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| Treatment protocol |
normal temperature and high temperature treatment
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were washed twice in Wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. 10 µL of concanavalin A coated magnetic beads (Bangs Laboratories) were added per sample and incubated at room temperature (RT) for 15 min. The bead-bound cells were resuspended in Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2 mM EDTA and a 1:50 dilution of the appropriate primary antibody. Primary antibody incubation was performed on a rotating platform for 2 hours overnight at 4 °C. Then, the secondary antibody was diluted 1:50 in Dig-Wash buffer and cells were incubated at RT for 30 min. The pA-Tn5 adapter complex was added to the cells with gentle vortexing, and incubated at RT for 1 h. Next, cells were resuspended in Tagmentation buffer (10 mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. Then, DNA extraction was performed with proteinase K digestion and the following purification with Ampure XP beads (Beckman Counter). Cut&Tag libraries were amplified with NEBNext HiFi 2× PCR Master mix (New England Biolabs, Inc., USA). Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).
CUT&Tag
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina Novaseq 6000 sequencer. Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.2) software, high quality reads were generated. Then these high quality reads were aligned to reference genome (galGal6) using bowtie2 software (v2.2.4). Peak calling was performed with MACS software (v1.4.2).
Genome_build: galGal6
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: enriched peaks
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| Submission date |
Sep 09, 2020 |
| Last update date |
Sep 10, 2020 |
| Contact name |
Ding Yu |
| E-mail(s) |
ding@rnastar.com
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| Organization name |
Newcore biotechnology
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| Street address |
Number 953 Jianchuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200000 |
| Country |
China |
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| Platform ID |
GPL26853 |
| Series (1) |
| GSE157728 |
CUT&Tag for analysis of Nrf2-regulated genes in liver of heat-stressed chicken (Gallus gallus) |
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| Relations |
| BioSample |
SAMN16089406 |
| SRA |
SRX9101064 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4773987_G16.bed.gz |
96.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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