|
| Status |
Public on Apr 20, 2022 |
| Title |
Gata1s-FLC+shArid3a_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Gata1s-FLCs
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Doxycycline 1μg/mL for 10 days
strain: B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J
developmental stage: day E12.5-13.5 p.c.
transgene1: sgGata1
transgene2: shArid3a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Quick-RNA Miniprep (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
shA_025.gz
Knockdown.genes.readcount.annot
|
| Data processing |
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
hisat 2 (v2.0.5.) was used to mapp to the reference genome (--dta --phred33)
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample
|
| |
|
| Submission date |
Mar 26, 2021 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Jan-Henning Klusmann |
| E-mail(s) |
jan-henning.klusmann@kgu.de
|
| Organization name |
Goehte University Frankfurt
|
| Department |
Pediatric Hematology and Oncology
|
| Street address |
Theodor-Stern-Kai 7
|
| City |
Frankfurt |
| ZIP/Postal code |
60590 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE169738 |
Chromosome 21-encoded miR-125b cooperates with GATA1s in trisomy 21-associated megakaryoblastic leukemia by targeting the megakaryocytic transcription factor ARID3A I |
|
| Relations |
| BioSample |
SAMN18510017 |
| SRA |
SRX10457591 |
