 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 10, 2022 |
| Title |
NP1-2 |
| Sample type |
SRA |
| |
|
| Source name |
gut
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: NP1/+
age: post natal day 3-5
tissue: gut
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNAseq in fly guts, around 20 guts of each sample were dissected in RNase-free PBS. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Bcl2fastq (v2.17.1.14) software used for basecalling.
Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: Drosophila melanogaster .BDGP6.95
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 01, 2021 |
| Last update date |
Aug 10, 2022 |
| Contact name |
HANSONG DENG |
| E-mail(s) |
HDENG@TONGJI.EDU.CN
|
| Phone |
+8617364161727
|
| Organization name |
Tongji University
|
| Street address |
RM 5O1, BLDG 1, # 817 ZHENGLI RD, YANGPU DISTRICT
|
| City |
SHANGHAI1 |
| ZIP/Postal code |
200085 |
| Country |
China |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE185159 |
Next Generation Sequencing Facilitates Quantitative Analysis of NP1 and NP1/CRTCHA Gut Transcriptomes |
|
| Relations |
| BioSample |
SAMN21973420 |
| SRA |
SRX12436173 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
