|
| Status |
Public on Aug 10, 2020 |
| Title |
PcGGLKD RNAseq_bam_E(z)GLKD_3 |
| Sample type |
SRA |
| |
|
| Source name |
PcGGLKD RNAseq_whole ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
uas-rnai: E(z)
gal4/uas: nos-Gal4
developmental stage: 7-10 day-old adult
tissue/cell type: whole bam ovary
spike-in normalization: none
library construction: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2
|
| Growth protocol |
flies were grown on standard food plus wet yeast paste for 3-6 days
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA prepared from whole ovaries expressing germline-specific RNAi, or from FACS-purified germline stem cells. Sequences were mapped to dmel 6.02 with Hisat2. Whole gene TPMs from Stringtie were aggregated into polyA_RNAseq_stringtieO.txt. For differential analysis, raw read counts from htseq-count were processed with DEseq2 and custom annotation, code at: github.com/ciwemb/polycomb-development
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
polyA_RNAseq_stringtieO.txt
ezGLKD_bam_3_TPM
|
| Data processing |
RNAseq: reads mapped with Hisat2.1.0, processed with Stringtie1.3.5
RNAseq: raw read counts per gene extracted with htseq0.10.0
ChIPseq: reads mapped with bowtie2.3.2
ChIPseq: MAPQ30 filtered with samtools1.6
ChIPseq: RPM normalized (additionally normalized to spike in if applicaple)
Genome_build: RNAseq: dmel6.02, Ensembl 81; ChIPseq: dmel6.02 (no spike in), dmel6.02/dpse3.0 (D. pseudoobscura spike-in), or dmel6.02/mm10 (mouse spike-in)
Supplementary_files_format_and_content: RNAseq: htseq are text files with raw readcounts, polyA_RNAseq_stringtieO.txt is txt file with TPMs for all genes/samples from stringtie
|
| |
|
| Submission date |
Feb 13, 2020 |
| Last update date |
Aug 10, 2020 |
| Contact name |
Allan C Spradling |
| E-mail(s) |
[email protected]
|
| Phone |
410 246-3015
|
| Organization name |
Carnegie Institution/HHMI
|
| Department |
Embryology
|
| Street address |
3520 San Martin Dr.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21218 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE145282 |
Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins |
|
| Relations |
| BioSample |
SAMN14100798 |
| SRA |
SRX7723681 |
