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Status |
Public on Aug 09, 2019 |
Title |
RNAseq_dNxf2_het_Panx_FL10B_rep1 |
Sample type |
SRA |
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Source name |
ovary
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Organism |
Drosophila melanogaster |
Characteristics |
age: 3-5 old tissue: ovary genotype: nxf2 +/-, panx FL10B tethered
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Treatment protocol |
Flies were fed with yeast. Germline specific knockdowns were done as described (Czech et al., 2013 Mol Cell). CRISPR/Cas9 mediated generation of dNxf2 mutants and Panx mutants were done as described (Port et al., 2014 PNAS).
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Growth protocol |
All fly stocks were maintained at 25°C on standard diet.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was prepared with Trizol reagent (Invitrogen), Transcriptome libraries were prepared according (Armour et al. 2009, Nat Methods) using not-so-random priming (NSR). 1 ug total RNA was revere transcribed using SuperScript III enzyme with first-strand NSR primer. RNA template was removed with RNase H (Invitrogen). Then cDNA was mixed with exo-Klenow fragment (NEB) second-strand NSR primer to synthesize the second strand. For PCR amplification, purified second-strand synthesis reaction were mixed with LA Taq Version 2.0 (Takara) and P5-SBS3T-NSR and P7-SBS8N-NSR primers. Products were run on a 2% low-melt agarose gel, and the 250–500 bp range were purified. RNA-seq was performed as described (Vagin et al., 2013 RNA and Armour et al., 2009 Nat Methods). Samples were sequenced on Illumina platforms with HiSeq X Ten.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Description |
RNAseq_gene.count.txt
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Data processing |
Basecalls were performed using bcl2fastq v1.8.4 for Illumina HiSeq 2500 and HiSeq X Ten output. RNA-seq reads (single-end reads or read1 for paired-end reads) were processed using Cutadapt (v1.16) . The adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and low-quality bases were trimmed from the 3’ end of reads, and reads short than 20 bp were discarded. RNA-seq reads were aligned to UCSC dm3 using STAR (v2.5.2a), only uniquely mapped reads were retained. To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format. Genome_build: dm3 Supplementary_files_format_and_content: bigWig files
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Submission date |
Apr 18, 2019 |
Last update date |
Aug 10, 2019 |
Contact name |
Ming Wang |
E-mail(s) |
wangming@ibp.ac.cn
|
Phone |
01064881022
|
Organization name |
Institute of Biophysics, Chinese Academy of Sciences
|
Department |
Key Laboratory of RNA Biology
|
Lab |
Yang Yu
|
Street address |
#15 Datun Road, Chaoyang, Beijing 100101, China
|
City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100101 |
Country |
China |
|
|
Platform ID |
GPL23702 |
Series (2) |
GSE121158 |
A Pandas complex adapted for piRNA-guided transposon silencing (RNA-seq) |
GSE130042 |
A Pandas complex adapted for piRNA-guided transposon silencing and heterochromatin formation |
|
Relations |
BioSample |
SAMN11463383 |
SRA |
SRX5709937 |