 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 22, 2022 |
| Title |
Differentiated cells, Day21, Bio rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
WA09
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WA09
cell type: Neural progenitor cells
genotype: TPH2-EGFP knockin
treatment: induced serotonin neuron differentiation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Approximately 10 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina（NEB，UK）following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Day21_2
|
| Data processing |
A cDNA library constructed by technology from the pooled RNA from < hESCs_1, hESCs_2, Day21_1, Day21_2, Day21_3, Day42_1, Day42_2, Day42_3> samples of homo sapiens was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: homo_sapiens GRCh38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 17, 2022 |
| Last update date |
Sep 22, 2022 |
| Contact name |
Ting Xu |
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE206341 |
Generation of a TPH2-EGFP reporter cell line for Purification and Monitoring of Human Serotonin neurons in vitro and in vivo |
|
| Relations |
| BioSample |
SAMN29176510 |
| SRA |
SRX15780015 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
