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Sample GSM7397964 Query DataSets for GSM7397964
Status Public on Jun 30, 2023
Title L3 animals with lin-29_NanoDam control, replicate 3
Sample type SRA
 
Source name Anchor Cell
Organism Caenorhabditis elegans
Characteristics tissue: Anchor Cell
sample type: Specific expression of Dam in target tissue
strain: DQM986
genotype: bmdSi244
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 lin-29_NanoDam_egl-43-vs-Dam.gatc.rep3.bedgraph
lin-29_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.peaks.rep3.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
Library strategy: DamID
 
Submission date May 19, 2023
Last update date Jun 30, 2023
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 (1)
GSE232946 NanoDam Profiling of EGL-43 in the Anchor Cell
Relations
BioSample SAMN35218419
SRA SRX20441092

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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