|
| Status |
Public on Jun 26, 2024 |
| Title |
XL_St11_5_NPB_Sox3_ChIP_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
animal pole explant
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: animal pole explant
cell line: Stage 11.5
cell type: neural plate border
genotype: wild type
treatment: Sox3 + Wnt8a +Chordin mRNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Animal pole explants were crosslinked for 15 minutes (10% formaldehyde (methanol-free)) and the fixation was quenched (125 mM glycine in PBSTr). Samples were lysed and sonicated and incbated with antibody overnight. Protein G Dynabeads were applied to sample for 1 hr and then washed in EDTA-free wash buffer before being tagemented with Tn5 transposase (40 min at 37C). Following tagmentation, samples were washed and reverse crosslinked. Qiagen MinElulte Reaction Clean Up kit was used to purify samples
Nextera primers and NEBNext Q5 master mix were used for library construction
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
S3_St11-5_NPB_ChIPpeaks_annotated.txt
|
| Data processing |
fastq files were trimmed using fastp and aligned using botwie2. Samtools was used to generate bam files. Picard was used to deduplicate bam files.
Genrich was used for peak calling on namesorted bam files (-t Sox3 samples -c Ctl samples -v -e MT -a 20.0 )
Assembly: Xenopus laevis 9.2
Supplementary files format and content: annotated bedfiles of Sox3 peaks (annoated using HOMER)
|
| |
|
| Submission date |
Jan 05, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Carole LaBonne |
| Organization name |
Northwestern University
|
| Department |
Molecular Biosciences
|
| Street address |
2220 Campus Drive
|
| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60208 |
| Country |
USA |
| |
|
| Platform ID |
GPL28901 |
| Series (2) |
| GSE252615 |
SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [ChIP-seq] |
| GSE252617 |
SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression |
|
| Relations |
| BioSample |
SAMN39276346 |
| SRA |
SRX23115282 |
