|
| Status |
Public on Jun 15, 2021 |
| Title |
w_eye_RNAPIIS2p_3_(20210223_KA_DmEc_1815_eye) |
| Sample type |
SRA |
| |
|
| Source name |
CUT&Tag
|
| Organism |
Drosophila melanogaster |
| Characteristics |
antibody: RNAPIIS2p Cell Signalling Technology cat#13499
genotype: w1118
tissue: dissected eye imaginal discs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cut-tag-with-drosophila-tissues-bnx5mfq6.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CUT&Tag for RNAPIIS2p in dissected eye imaginal discs from w1118 larvae
|
| Data processing |
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to dm6 Drosophila melanogaster genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file dm6_fragments.bed.gz). 3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (137567484) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).
|
| |
|
| Submission date |
Jun 11, 2021 |
| Last update date |
Jun 17, 2021 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE161919 |
The H3.3K27M oncohistone antagonizes reprogramming in Drosophila |
|
| Relations |
| BioSample |
SAMN19677429 |
| SRA |
SRX11124243 |
