 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 01, 2021 |
| Title |
Control_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
rat testis
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: testis
age: 8 weeks
experimental desgin: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Ribosomal RNA was removed using the Epicentre Ribo-Zero™ Gold kit (Rat) (Epicentre, an Illumina company, Madison, WI, USA). These libraries were constructed based on the recommendations of the NEBNext®Ultra™ Directed RNA Library Preparation Kit. RNA fragments and short-stranded RNA were carried using NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using a random hexamer primer and M-MuLV reverse transcriptase. Subsequently, second strand cDNA was synthesized using DNA polymerase I and RNase h, the purified second strand cDNA ends were repaired, and then poly(A) and A adapters were added. A fragment of approximately 300 base pairs (bp) was selected using the UNG enzyme.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The raw reads generated by RNA-seq were processed by removing the Illumina adapters with Trimmomatic and then low-quality regions at the 5' and 3' ends were deleted.
The reads (stored in fastq format) were then aligned to the rat (RGSC/rn6) reference genome Rnor_6.0, downloaded from Ensembl (ftp://ftp.bl.org/pub/relee-a-/rattus_norvegicus/), using HISAT2
Sorted bam files were quantified for gene expression using the HTseq-count tool , and a counts file was generated
Counculat TPM with Internal scripting
Genome_build: RGSC/rn6
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM values for each Sample
|
| |
|
| Submission date |
Jan 29, 2020 |
| Last update date |
May 02, 2021 |
| Contact name |
Pengxiang Tian |
| E-mail(s) |
tpx1234@126.com
|
| Organization name |
The second hospital of hebei medical university
|
| Street address |
215 heping west road
|
| City |
shijiazhuang |
| State/province |
hebei |
| ZIP/Postal code |
050000 |
| Country |
China |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE144485 |
Changes in Expressions of Spermatogenic Marker Genes and Spermatogenic Cell Population Caused by Stress |
|
| Relations |
| BioSample |
SAMN13940698 |
| SRA |
SRX7647626 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4289045_c1.txt.gz |
509.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
