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Sample GSM2632028 Query DataSets for GSM2632028
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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