|
| Status |
Public on Sep 16, 2019 |
| Title |
Wild-type-2_1_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type-2_1_RNASeq
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: Wild-type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP-seq data: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody; RNA-seq data: RNA was harvested using Trizol reagent
ChIP-seq data: (1) DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor.(2) PCR amplification and size selection (usually 100-300bp, including adaptor sequence). (3) Qualified library for sequencing. ; RNA-seq data: 1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
featureCounts_H4K91E_WildType.txt
|
| Data processing |
H4K91glu and input control ChIP-seq data (50bp sequence reads) were aligned to the human reference genome (hg19) using Burrows-Wheeler Aligner (BWA, version 0.7.17-r1188). To obtain an input-normalized BigWig files needed for the profile analysis, DeepTools (version 3.2.0) was applied.
Raw reads of RNA-seq data in FASTQ sequencing files were aligned by STAR (version 2.5.2b) aligner to the Saccharomyces cerevisiae reference genome (sacCer3). Read counts were generated by featureCounts (version 1.6.2).
Genome_build: ChIP-seq data: hg19
Genome_build: RNA-seq: sacCer3
Supplementary_files_format_and_content: For ChIP-seq data BigWig files were generated using deepTools
Supplementary_files_format_and_content: For RNA-seq data table with read counts were generated by featureCounts
|
| |
|
| Submission date |
May 28, 2019 |
| Last update date |
Sep 16, 2019 |
| Contact name |
Jason Wong |
| E-mail(s) |
jwhwong@hku.hk
|
| Phone |
+852 3917 9187
|
| Organization name |
The University of Hong Kong (HKU)
|
| Street address |
L1-51, Laboratory Block, 21 Sassoon Road
|
| City |
Hong Kong |
| State/province |
42-100 |
| ZIP/Postal code |
00000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL25927 |
| Series (1) |
| GSE131807 |
Glutarylation of Histone H4 Lysine 91 Regulates Chromatin Dynamics |
|
| Relations |
| BioSample |
SAMN11870800 |
| SRA |
SRX5905586 |
