|
| Status |
Public on Apr 15, 2024 |
| Title |
LT-HSCs_Ikba_Het_3 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
E14.5 foetal liver
|
| Organism |
Mus musculus |
| Characteristics |
developmental time: E14.5
tissue: foetal liver
cell type: 500 LT-HSCs
Sex: Female
condition: HET
|
| Growth protocol |
Primary LT-HSCs from foetal liver were obstained by disection follwed by FACS sorting directly into RTLplus Buffer.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Direct RNA isolation with RNeasy Mini Kit [Qiagen Ref. 74004]
Samples were processed to obtain cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020).
Trimmed reads were aligned to reference genome (GRCm38 release 102 from Ensembl) with STAR aligner tool (v2.7.8). STAR was executed with default parameters except for the number of allowed mismatches which was set to 1
Uniquely mapped reads were considered for further analysis. Raw gene expression was directly quantified in STAR with --quantMode GeneCounts option.
Raw counts matrix was imported into R Statistical software (v4.2.1). Prior to statistical analysis, those genes with less than 10 raw counts across the 8 samples per timepoint were discarded
For visualization purposes, counts were normalized by variance-stabilizing transformation method as implemented in DESeq2 R package (v1.38.3)
Assembly: mm10
Supplementary files format and content: Tab-separated value file: RNAseq_All_samples_Raw_counts.txt: RNAseq Raw expression levels for each gene (55,487 rows) in each individual sample as obtained from STAR. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_Norm_counts_Gender_corrected.txt. Normalized expression levels including the expression of 20,610 genes (rows) per all individual samples. Normalization carried out with VST from DESeq2 (v1.38.3)
|
| |
|
| Submission date |
Nov 10, 2021 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Anna Bigas |
| E-mail(s) |
abigas@imim.es
|
| Phone |
+34933160440
|
| Organization name |
Institut Hospital del Mar d'Investigacions Mèdiques
|
| Department |
Cancer Research
|
| Lab |
Stem Cells and Cancer
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE188523 |
A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development [RNA-seq] |
| GSE188525 |
A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development |
|
| Relations |
| BioSample |
SAMN23026394 |
| SRA |
SRX13095190 |
