|
| Status |
Public on Feb 03, 2020 |
| Title |
rip_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: nos-gal4/UASz-Flag-Yps
tissue: Ovary
|
| Treatment protocol |
NA
|
| Growth protocol |
Drosophila cultured at 29 degree for 3 days, ovaries were dissected and diassociated with type II collagenase, and mature eggs were fltered and discarded.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For M5C-seq, total RNA were extracted with Qiagen RNeasy Midi Kit and RNA were isolated with antibody. For RIP-seq, tissues were lysated with 1X polysome lysis buffer and RNA-protrein complexes were isolated with antibody.
Libraries were prepared according to TAKARA SMARTer RNA-Seq Pico Input kit
M5C-seq/RIP-seq
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Anti-Flag pull down
|
| Data processing |
cDNA libraries were prepared using SMARTer RNA-Seq Pico Input kit and sequenced as 75bp paired-end reads on Illumina Nextseq 500 machine. Raw sequencing reads were demultiplexed into Fastq file format using Illumina’s bcl2fastq v2.20.
Reads were aligned to UCSC genome dm6 with STAR aligner (version STAR_2.6.1c), using Ensembl 96 gene models.
Only uniquely mapped reads were selected for downstream analysis using Samtools. Duplicated reads were also removed using Picard to correct PCR amplification bias between samples.
Genome_build: dm6
Supplementary_files_format_and_content: Bigwig files
|
| |
|
| Submission date |
Nov 01, 2019 |
| Last update date |
Feb 03, 2020 |
| Contact name |
Shiyuan (Cynthia) Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Department |
Computational Biology
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE139828 |
Drosophila YBX1 homolog YPS promotes ovarian germline stem cell development by preferentially recognizing 5-methylcytosine RNAs |
|
| Relations |
| BioSample |
SAMN13178616 |
| SRA |
SRX7085380 |
