|
| Status |
Public on Aug 10, 2020 |
| Title |
sorted germcell ChIPseq_St5NC_PclGLKD_Pse_In |
| Sample type |
SRA |
| |
|
| Source name |
sorted germcell ChIPseq_FACS purified germ cell
|
| Organism |
Drosophila melanogaster |
| Characteristics |
uas-rnai: Pcl
gal4/uas: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato
developmental stage: 3-6 day old adult
tissue/cell type: FACS-purified 64C germ cells
chip antibody: Input
spike-in normalization: Drosophila pseudoobscura follicle cells
library construction: DNA libraries prepared with Takara Bio ThruPLEX DNA seq
|
| Growth protocol |
flies were grown on standard food plus wet yeast paste for 3-6 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FACS-purified Drosophila melanogaster germ cells were mixed with either FACS purified Drosophila pseudoobscura follicle cells, mouse embryonic fibroblasts, or in some cases, no spike-in. Sequences were mapped to the D.mel6.02 genome or a hybrid genome of D.mel6.02/D.pse3.0 or D.mel /M.m10 and MAPQ 30 filtered. The ratio of Spike-in to D.mel reads was used to normalize enrichment between IP samples and normalized genome wide read coverage was calculated with Bedtools and supplied as a bigWig file for each sample. Normalized read depth was also was also calculated for overlapping 5kb bins annotated with a 3 or 4 state chromatin model and supplied as a modified bed file.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
4state_enrichment_counts.txt
|
| 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 |
SAMN14100784 |
| SRA |
SRX7723691 |
