|
| Status |
Public on Sep 04, 2020 |
| Title |
YueLab-RNA-Seq-Colon-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Tissue
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tuebingen
tissue: Colon
|
| Growth protocol |
Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For each RNA-seq experiment, the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk, ten 1-dpf fish were dechorionated with pronase and trunk were cut off for RNA-seq. For embryonic neuron, green cells from Tg(Huc:Kaede) cells were sorted by FACS and approxinately 20,000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol (Invitrogen).
The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s protocol. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads (Invitrogen). Extracted RNA was first fragmented, then followed by reverse transcription, end repair, adenylation, adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 50 bp high-throughput sequencing using HiSeq 2500 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
YueLab-RNA-seq-Colon_merged.TPM.txt
|
| Data processing |
RNA-seq reads were aligned to zv10 genome assembly using STAR;
ChIP-seq and ATAC-seq reads were aligned to zv10 genome assembly using BWA
HiC reads were aligned to zv10 genome assembly using Bowtie2
The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq peaks were called using MACS2 with the following setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5
HiC matrix was generated using HiC-Pro
Genome_build: zv10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.**All replicates were merged
|
| |
|
| Submission date |
Jul 09, 2019 |
| Last update date |
Sep 04, 2020 |
| Contact name |
Yu Luan |
| E-mail(s) |
yu.luan@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Department of Biochemistry and Molecular Genetics
|
| Lab |
Feng Yue
|
| Street address |
303 E. Superior Simpson Querrey 7-518
|
| City |
CHICAGO |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL10164 |
| Series (1) |
| GSE134055 |
A map of cis-regulatory elements and 3D genome structures in zebrafish |
|
| Relations |
| BioSample |
SAMN12239149 |
| SRA |
SRX6422892 |
