|
Status |
Public on Feb 04, 2022 |
Title |
iAKI Hoxb7 Pulldown 2 |
Sample type |
SRA |
|
|
Source name |
Pulldown of TU tagged Kidney RNA
|
Organism |
Mus musculus |
Characteristics |
treatment: iAKI Sex: f rna tag: 4-TU genotype: Hoxb7Cre;UPRTf/+ age: 5.5 months tissue: kidney
|
Treatment protocol |
4-TU (430 mg/kg body weight; ip) was administered 4 hours prior to kidney dissection and RNA isolation.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was purified with Trizol. 4-TU tagged RNA was biotinylated by EZ-link Biotin HPDP (1 mg/ml, Pierce Biotechnology) in N,N-dimethylformamide (DMF, Sigma) for 30min and for 3 hours with EZ-link Biotin HPDP (0.2 mg/ml) in 1 ml of 10 M Tris/HCl, pH7.5, 1mM EDTA for every 100μg of total RNA. RNA was mixed with streptavidin beads (100μl, Miltenyi Biotec Inc), and applied to magnetic columns (Miltenyi Biotec Inc). Biotinylated RNA was eluted with 5% (v/v) β-mercaptoethanol. We finally used RNeasy MinElute Cleanup Kit (Qiagen) to concentrate the biotinylated RNA. Library prepared by using Illumina TruSeq RNA prep kit
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
BT002 Barcode: CCGTCC
|
Data processing |
Illumina RTA was used to perform base calling, and CASAVA (version 1.8.2) was used for converting base call files (.BCL) to FASTQ format and for performing sequence adaptor trimming. Reads were then trimmed using Trimmomatic version 0.36 (LEADING:10 TRAILING:10 MINLEN:30). Reads were aligned to the mouse reference genome (mm10) using STAR aligner version 2.5.3a (default settings). Count tables were generated with HTSeq (version 0.6.1p2) using default settings. Genome_build: mm10 Supplementary_files_format_and_content: count matrix table csv file with the raw counts generated by HTSeq for all samples
|
|
|
Submission date |
May 19, 2017 |
Last update date |
Feb 04, 2022 |
Contact name |
Jacob Stauber |
E-mail(s) |
jacobstauber1@gmail.com
|
Organization name |
Columbia University
|
Lab |
Jonathan Barasch
|
Street address |
1150 Saint Nicholas Ave., Russ Berrie Bldg. Rm.408A
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10032 |
Country |
USA |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE99084 |
A Snapshot of RNA Expression in a Single Segment of the Kidney Reveals Stimulus Specific Responses |
|
Relations |
BioSample |
SAMN07142697 |
SRA |
SRX2834672 |