|
| Status |
Public on May 01, 2024 |
| Title |
Exp#1_Bre1_RIP_0317 |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Ovary
strain: Oregon-R
genotype: wild type
antibody: anti-Bre1
|
| Treatment protocol |
Ovarian lysate collected from young females was spited into three parts for adding anti-IgG, anti-Lsd1 and anti-Bre1 antibody respectively.
|
| Growth protocol |
Oregon-R flies were raised under standard fly culture condition. For each RIP experiment, ~200 young females (12hr post eclosion) were collected for dissecting out oavries.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Collected ovaries were transferred into RIP buffer and then homogenized, lysed, and centrifuged to acquire ovarian lysate.
Library was prepared using iIlumina TruSeq RNA Sample Prep Kit v2 (Guide Revision F). The polyA selection steps were skipped, and samples were proceed directly to Fragmentation and Priming and cDNA synthesis.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
For Exp#1, sequenced reads were trimmed for adaptor sequence, and mapped to dm6 whole genome using tophat (Bowtie2 [2.0.6.0] and Samtools [0.1.18.0]); For Exp#2, sequenced reads were trimmed for adaptor sequence, and mapped to dm6 whole genome using CLC Genomics Workbench 11.0.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.
Assembly: dm6
|
| |
|
| Submission date |
Oct 08, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Ming-Chia Lee |
| E-mail(s) |
lee.mingchia@nycu.edu.tw
|
| Organization name |
National Yang Ming Chiao Tung University
|
| Department |
Department of Life Sciences and Institute of Genome Sciences
|
| Lab |
Lab of Molecular Epigenetics
|
| Street address |
Library, Info & Research Bldg, Rm 904 #155, Sec. 2, Li-Nong St
|
| City |
Taiepi |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE244906 |
To survey ncRNAs that associate with Lsd1 or Bre1 complexes through RIP experiments |
|
| Relations |
| BioSample |
SAMN37724337 |
| SRA |
SRX22029192 |
