|
| Status |
Public on Apr 03, 2021 |
| Title |
LEF1_WntMO_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Neural folds
|
| Organism |
Gallus gallus |
| Characteristics |
developmental stage: HH9
genotype: Wnt knockdown
antibody: Abcam, #ab137872
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neural folds were dissected from HH9 morphant embryos (n=20 per CUT&RUN experiment). Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CUT&RUN data for LEF1 in chick neural crest cells at specification stage (HH9) upon Wnt knockdown
|
| Data processing |
Library strategy: CUT&RUN
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal5 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.
|
| |
|
| Submission date |
May 06, 2020 |
| Last update date |
Apr 03, 2021 |
| Contact name |
Marcos Simoes-Costa |
| E-mail(s) |
simoescosta@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Simoes-Costa Lab
|
| Street address |
526 Campus Rd
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE150006 |
The connectome of neural crest enhancers reveals regulatory features of signaling systems |
|
| Relations |
| BioSample |
SAMN14845430 |
| SRA |
SRX8279265 |
