|
| Status |
Public on Oct 15, 2017 |
| Title |
H3D_H3H_0_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
YPH500
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YPH500
genotype: histone H3 mutant H3A110D/H3L130H
replicate number: Replication 2
starvation duration: glucose starvation for 0 hr(s)
|
| Growth protocol |
samples were grown in YPD to mid-log phase and then shifted to medium containing 0.05% glucose for one-hour induction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from yeast cells was isolated by RNeasy midi kit (Qiagen).The mRNA was purified from total RNA by Dynal oligo(dT) beads (Invitrogen).
The first and second strand cDNA was synthesized by SuperScript III CellsDirect™ cDNA Synthesis Kit (Invitrogen) and SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen), respectively; the resulting double strand cDNAs were followed by DNA repair and end-polishing (blunt-end) with End-It DNA End-Repair Kit (Epicentre), purified with QIAquick PCR Purification Kit(Qiagen), and dA-tailed utilizing the 3´-5´ exo-Klenow Fragment (NEB),the resulting purified fragments were ligated to adaptor oligo mix (Illumine) using Quick T4 DNA ligase (NEB). The 200-500 bp ligation products were recovered from a 2% (w/v) agarose gel using Qiagen gel extraction kit. Then followed by a PCR amplification with Solexa primers using KAPA HiFiTMHotStart kit. The 250-400 bp amplified products were purified again from a 2% agarose gel and used directly for high throughput sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: normalized_abundance_H3D_H3H_0_1.txt
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
For the raw sequence data, we trimmed the top 15 bp, using tophat (v2.0.11) only mapping the reads to the transcriptome of sacCer3 (Apr. 2011) with the default parameter.
For the mapped reads, we then extracted the reads which have the “NH:i:1” field. In order to reduce the PCR duplicates’ bias, in here, we only keep 1 record at the same position.
The aligned reads were analyzed using the Cuffdiff2 (v2.2.1) to determine the RPKM (Reads PerKilobase of transcript per Millionmapped reads) value in each sample. Besides, we also calculate the average RPKM value of the sample put two replicates together.
Genome_build: sacCer3 (Apr. 2011)
Supplementary_files_format_and_content: text file with RPKM values for each replicate and average RPKM of two replicates.
|
| |
|
| Submission date |
Oct 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Qiu Zhou |
| E-mail(s) |
jqzhou@sibcb.ac.cn
|
| Phone |
021-54921076
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences
|
| Street address |
320 Yueyang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE88878 |
RNA transcription profile of different yeast mutants under glucose starvation (0.05% glucose) |
| GSE104313 |
Independent manipulation of histone H3 modifications in individual nucleosomes reveals the contributions of sister histones to transcription |
|
| Relations |
| BioSample |
SAMN05916170 |
| SRA |
SRX2250629 |
