|
| Status |
Public on May 29, 2024 |
| Title |
L3 animals with dat-1_NanoDam control, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Dopaminergic Neurons
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Dopaminergic Neurons
sample type: Specific expression of Dam in target tissue
strain: TV27654
genotype: bmd261
developmental stage: L3
|
| Growth protocol |
Animals grown for 3 generations on Dam- bacteria (E. coli ER2925 from NEB) were bleach synchronized and L1s were grown at 25C until the L3 stage (24h after putting L1s on food). Approximately 5000 synchronized worms were harvested, washed with M9, then snap frozen in liquid nitrogen and stored at -80C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was harvested using a Qiagen DNeasy Tissue and Blood kit (#69504) with no deviations from standard protocols.
DamID amplicons were obtained as previously described (Gomez-Saldivar et al., 2021) using 4 initial PCR cycles followed by 19 additional cycles. DamID amplicons were directly barcoded through blunt end ligation and sequenced using Oxford Nanopore library reagents (LSK-109, NBD-104, NBD-114)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Description |
MinION Mk1C
dat-1_NanoDam_Alone_rep1
Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep1.bedgraph
Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep1.peaks.gff
Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep1.bedgraph
Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep1.peaks.gff
|
| Data processing |
Nanopore sequences were basecalled and demultiplexed using guppy 3.6 onboard a MinION Mk1C device, only base calling reads with a Q score higher than 8.
Fastq files were combined together using the UNIX command 'cat' and mapped to the ce10 genome using minimap2 with the options '-ax map-ont' to output .sam files.
SAM files were sorted and converted to bam using samtools.
Sorted .bam files and a file mapping all GATC sequences in C. elegans were fed into damidseq_pipeline (Marshall and Brand, 2015) to obtain bedgraph files.
Bedgraphs were analyzed for peaks using find_peaks (Owen Marshall).
Assembly: ce10
Supplementary files format and content: .bedgraphs represent the comparisons between the NanoDam alone control vs. NanoDam binding to a transcription factor
Supplementary files format and content: .gff files represent the called peaks after analysis of the .bedgraph files
|
| |
|
| Submission date |
Mar 16, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
Callista Yee |
| E-mail(s) |
calyee@stanford.edu
|
| Organization name |
Stanford University/HHMI
|
| Street address |
327 Campus Drive, Shen lab, Bass Biology 329
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL26522 |
| Series (2) |
| GSE227552 |
NanoDam Profiling of EGL-43 and FOS-1 in Dopaminergic Neurons |
| GSE260637 |
An activity regulated transcriptional program directly drives synaptogenesis |
|
| Relations |
| BioSample |
SAMN33788189 |
| SRA |
SRX19695562 |
