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Status |
Public on Nov 22, 2017 |
Title |
G1S RNA-seq rep2 |
Sample type |
SRA |
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Source name |
late embryonic cell line
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Organism |
Drosophila melanogaster |
Characteristics |
cell line: S2R+ developmental time: embryo 20-24h drug for synchronization: Hydroxyurea
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Growth protocol |
Drosophila late embryonic S2R+ cells were seeded at the density of 1X 10^6 cells/ml and grown in Schneider's medium ( Invitrogen) with 10% heat-inactivated fetal bovine serum (BI) at 25 °C. Cells were synchronized at G1/S by incubating with 1 µM Hydroxyurea (HU) for 18 h
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA were extracted with Trizol reagent. PolyA+ RNA-seq libraries were prepared using KAPA Stranded mRNA-seq kit following the manufacturer’s instructions.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Data processing |
The two ends of the Hi-C reads were seperately mapped to the Drosophila melanogaster dm3 reference genome using Bowtie2(v2.2.9). An iterative mapping method was adopted with an initial length 25bp, if this region failed to map uniquely, an additional 25 bp was included in the next round of mapping. This procedure was continued until the full read length reached 150 bp. Only reads with high mapping quality(MAPQ>30) were kept for further analysis. Reads mapped to the same restriction fragment and dangling reads seperated by less than 500bp and PCR duplicates were further removed. The Hi-C contact maps were normalized using ICE(Imakaev et al, 2012), restriction fragments were treated as units instead of equally spaced bins. Domains were called using Armatus(Filippova et al, 2014) with scaling parameter, gamma, set to 0.9. Domains interrupted by gaps were modified locally using gamma 0.6. Adapters and low quality reads were removed by cutadapt (v1.8.3) and Trimmomatic (v0.36) using default parameters. Valid paired reads were mapped to the Drosophila melanogaster reference genome dm3 and Flybase gene annotation v5.57 using Tophat2 (v2.0.9) with default options and transcripts were assembled using Cufflinks (v2.2.1). Two replicates were merged for further analysis. Genome_build: dm3 Supplementary_files_format_and_content: S2Rplus_G1S_domain.txt is a tab-delimited text file contains domain positions in synchronized G1S S2R+ cells. G1S_genes.txt is a tab-delimited text file contains positions, ids, names and expression levels(FPKM) of Flybase r5.57 annotated genes .
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Submission date |
Jul 12, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Qi Wang |
E-mail(s) |
rubbyqi@sjtu.edu.cn
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Organization name |
Shanghai Jiaotong University
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Street address |
800 Dong Chuan Rd.
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City |
Shanghai |
State/province |
Shanghai |
ZIP/Postal code |
200240 |
Country |
China |
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Platform ID |
GPL23702 |
Series (1) |
GSE101317 |
Sub-kb resolution Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells |
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Relations |
Reanalyzed by |
GSM3283806 |
BioSample |
SAMN07346458 |
SRA |
SRX2997991 |
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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