 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 23, 2024 |
| Title |
L1777_4_2 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Solanum habrochaites |
| Characteristics |
tissue: leaves
treatment: cold
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were prepared using sucrose sedimentation as previously reported but with slight modifications.
Briefly, the young leaves of AC and LA1777 were collected under normal conditions or under cold stress for 6 h, respectively, and then ground to fine powder in liquid nitrogen. For each sample, 0.2 g of the frozen tissue powder was homogenized in prechilled 1 ml lysis buffer (15 mM Tris-HCl pH7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 5 mM 2-ME, 0.2% TritonX-100), and the nuclear fraction was purified as described47. The nuclei pellet was resuspended in 1 ml cold lysis buffer. For ATAC-seq and ATAC-qPCR, a nuclei aliquot (25 µl) was stained with DAPI (10 µl of 1 µg ml-1) and counted using a haemocytometer. Approximately 50000 nuclei were used for each ATAC-seq or ATAC-qPCR reaction.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Briefly, nuclei were extracted and purified from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads (Beckman, A63881) and library quality was assessed with Qubit (Thermo Fisher, Q32854). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform at Metware Biotechnology (Wuhan, China) and 150 bp paired-end reads were generated.
Assembly: Reference genome and gene model annotation files were downloaded from tomato genome website (https://solgenomics.net/) directly.
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Feb 02, 2024 |
| Last update date |
Feb 23, 2024 |
| Contact name |
Mingyue Guo |
| E-mail(s) |
21916052@zju.edu.cn
|
| Phone |
+8618143465226
|
| Organization name |
浙江大学
|
| Street address |
浙江大学紫金港校区
|
| City |
杭州市 |
| State/province |
浙江省 |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL34161 |
| Series (1) |
| GSE254893 |
Combined analysis of ATAC-Seq and RNA-Seq reveal a potential role of WRKY34 in tomato response to cold stress [ATAC] |
|
| Relations |
| BioSample |
SAMN39744087 |
| SRA |
SRX23506679 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8059879_L1777_4_2.bw |
131.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
