|
| Status |
Public on Mar 12, 2020 |
| Title |
All-tissue_72hpa_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
tadpole tail tissue
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: tadpole tail
regeneration timepoint: 72 hours post amputation
stage amputated: NF Stage 41 (3 days post fertilization)
genotype: Xtr.Tg(pax6:GFP;cryga:RFP;actc1:RFP)
|
| 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 |
W723
peaks_counts.txt
ALL_merged_summits.bed
|
| 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
|
| |
|
| Submission date |
Mar 11, 2020 |
| Last update date |
Mar 12, 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 (2) |
| GSE146830 |
Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors |
| GSE146837 |
Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors |
|
| Relations |
| BioSample |
SAMN14360577 |
| SRA |
SRX7897957 |
