|
| Status |
Public on Sep 23, 2020 |
| Title |
WT_0hpa_FACS [S2] |
| Sample type |
SRA |
| |
|
| Source name |
tadpole tail tissue
|
| Organism |
Xenopus tropicalis |
| Characteristics |
genotype: Wildtype
regeneration timepoint: 0hpa
tissue: tadpole tail tissue
facs: FACS
|
| Treatment protocol |
The posterior third of an anestitized tadpole tail was amputated at NF stage 41. Tadpoles were replaced in media without anesthetiz and allowed to regenerated until desired collection timepoint.
|
| Growth protocol |
Xenopus were reared in 1/9 Modified Ringers solution at 23C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The regenerated tail was isolated from the tadpole and cells were dissociated into single cell suspension using Liberase, washed in PBS and sorted for fluoresence through an Aria III cell sorter.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2_SG_Wills_03_WT_0hpa_S2
|
| Data processing |
Trim Galore!
Trim sequencing adaptors from fastq files
trim_galore --paired --phred33 --trim1 --nextera ${fastqDIR}${file}_R1_001.fastq.gz ${fastqDIR}${file}_R2_001.fastq.gz --output_dir
Bowtie2
align reads to the genome
bowtie2 --very-sensitive -x ${GenomeDIR} -X 2000 2>> ${BAMDIR}bowtie_log.txt -p 1 -1 ${fastqDIR}trimmed/${file}_R1_001_val_1.fq.gz -2 ${fastqDIR}trimmed/${file}_R2_001_val_2.fq.gz | samtools view -Sb - | samtools sort - -o ${BAMDIR}${file}.bam
MACS2
call peaks on aligned reads
macs2 callpeak -t ${BAMDIR}${file}.bam --nomodel --shift -100 --extsize 200 -g 1.7e9 -f BAM -n ${file} --outdir ${MACSDIR}${file}
GenomicRanges
annotated peaks to nearest transcription start site
used: Xtropicalisv9.0.Named.primaryTrs.gff3 for annotation
Rsubread
make counts matrix for all samples
featureCounts(isPairedEnd=TRUE, maxFragLength=2000)
Genome_build: Xtropicalis9.0
Supplementary_files_format_and_content: peak counts
|
| |
|
| Submission date |
Sep 22, 2020 |
| Last update date |
Sep 23, 2020 |
| Contact name |
Anneke Dixie Kakebeen |
| E-mail(s) |
akakebee@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Biochemistry
|
| Lab |
Andrea Wills
|
| Street address |
5611 9th Ave NW
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98107 |
| Country |
USA |
| |
|
| Platform ID |
GPL24884 |
| Series (1) |
| GSE158331 |
Tissue disaggregation and isolation of specific cell types from transgenic Xenopus appendages for transcriptional analysis by FACS |
|
| Relations |
| BioSample |
SAMN16237125 |
| SRA |
SRX9171386 |
