|
| Status |
Public on Jul 08, 2021 |
| Title |
wild-type_2_dTAG |
| Sample type |
SRA |
| |
|
| Source name |
hematopoietic cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived hematopoietic cells
genotype: parental
condition: dTAG
identifier: WT_2_dTAG
batch: HEM19
factor combined: parental_dTAG
|
| Treatment protocol |
differentiating cells were treated for the first day with 3µM CHIR99021 and 11 days either with 100nM dTAG-13 or DMSO vehicle
|
| Growth protocol |
hiPSCs were grown on Matrigel in mTeSR1 medium and differentiated for 12 days with StemDIFF hematopoietic kit
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent with glycogen as co-precipitant
polyA-enrichment + stranded NEBNext Ultra II kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
104155
|
| Data processing |
demultiplexed bam files were obtained from the squencing facility
bam to fastq conversion, picard toolsSamToFastq, version 2.7.1-SNAPSHOT
reads were mapped to human genome GRCh38 without alt loci using STAR 2.7.0b
Count statistics for Refseq genes were obtained by the “featureCounts” function (package Rsubread_1.28.1) using Ensembl annotation Homo_sapiens.GRCh38.100
Gene expression was normalized, batch-corrected and analyzed using DESeq2 version 1.18.1; design "~batch + combined"; including independent filtering with alpha=0.05, cooksCutoff=FALSE; shrunken log2 fold changes using the adaptive shrinkage estimator were calculated
Genome_build: GRCh38 without alt loci ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.g2z
Supplementary_files_format_and_content: raw_counts.txt: Matrix table with raw read counts for every gene and every samples
Supplementary_files_format_and_content: normalized_counts.txt: table including normalized counts for transcripts with gene symbol only; further filtered according to independent filtering alpha=0.05
Supplementary_files_format_and_content: LFC_padj.txt: table including shrunken Log2FC + padj
|
| |
|
| Submission date |
Oct 08, 2020 |
| Last update date |
Jul 08, 2021 |
| Contact name |
Klaus Josef Fortschegger |
| E-mail(s) |
[email protected]
|
| Organization name |
St. Anna Kinderkrebsforschung
|
| Department |
Genetics of Leukemia
|
| Lab |
Strehl
|
| Street address |
Zimmermannplatz 10
|
| City |
Vienna |
| State/province |
Austria |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE159261 |
Expression of RUNX1-JAK2 in Human Induced Pluripotent Stem Cell-Derived Hematopoietic Cells Activates the JAK-STAT and MYC Pathways. |
|
| Relations |
| BioSample |
SAMN16398834 |
| SRA |
SRX9266272 |
