 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 18, 2021 |
| Title |
AD2_3_mid |
| Sample type |
SRA |
| |
|
| Source name |
intestinal stem cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: intestine
developmental stage: Middle-aged adult (29-31 days old)
genotype: W Dah ; esg-Gal4, UAS-2xEYFP; Su(H)GBE-Gal80
|
| Treatment protocol |
Flies were aged to indicated time-points (young, middle-aged and old), at which point they were dissected and intestinal stem cells were isolated.
|
| Growth protocol |
Flies were raised and maintained on a standard yeast/molasses diet and kept at 25°C with 65% humidity on a 12 hour light/dark cycle.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Midguts of ~100-140 flies were dissected and dissociated using 0.5% Trypsin-EDTA and 100,000 YFP-labeled intestinal stem cells were isolated using FACS. Cells were collected into PBS and immediately spun down at 4°C, washed and lysed to release nuclei, which were then transposed using the Nextera DNA Sample prep kit (Illumina) according to manufacturer's instructions.
Transposed DNA was purified using MiniElute Reaction Cleaup kit (Qiagen). Transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs). Libraries were quantified by qPCR to determine the cycle number at which each sample produced 25% of maximum fluorescent intensity. The fluorescent intensity was used to estimate the number of additional PCR cycles required for each sample.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
AD2_3_mid
|
| Data processing |
remove short and low quality reads: Trimmomatic. Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence.Data. Bioinformatics, btu170.
remove mitochondria originated reads: bowtie2, SAMtools 1.7. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-359. Published 2012 Mar 4. doi:10.1038/nmeth.1923; [4] Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352
remove reads mapped to black listed regions: BEDTools' intersect utility. https://github.com/Boyle-Lab/Blacklist/tree/master/lists
merge alignments from samples of the same experimental condition: SAMtools' merge utility. Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352
genomic coverage: deepTools bamcoverage utility. Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. “deepTools2: a next generation web server for deep-sequencing data analysis.” Nucleic Acids Research (2016): gkw257
Identify open genomic areas: ENCODE recommended pipeline, developed by Anshul Kundaje's lab at Stanford University. https://github.com/ENCODE-DCC/atac-seq-pipeline
Genome_build: dm6: Full genome sequences and annotations for Drosophila melanogaster (Fly) as provided by UCSC (dm6, Aug. 2014) http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Drosophila_melanogaster/UCSC/dm6/Drosophila_melanogaster_UCSC_dm6.tar.gz
|
| |
|
| Submission date |
Jan 05, 2021 |
| Last update date |
Mar 18, 2021 |
| Contact name |
Tal Ronnen Oron |
| E-mail(s) |
talronor@gmail.com
|
| Organization name |
Buck Institute for Research on Aging
|
| Department |
Bioinformatics Core
|
| Street address |
8001 Redwood blvd.
|
| City |
Novato |
| State/province |
CA |
| ZIP/Postal code |
94945 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE157796 |
Aging ISCs and Polycomb KD ISCs |
| GSE164317 |
Age-related changes in Pc gene regulation disrupt lineage fidelity in intestinal stem cells |
|
| Relations |
| BioSample |
SAMN17219065 |
| SRA |
SRX9786718 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5006282_mid1_filtered_RPGC.bigwig |
29.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
