 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 01, 2023 |
| Title |
187484 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA-Seq Pro-B cell WT
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
chip antibody: n.a.
cell type: Pro-B cell
genotype: WT
treatment: Ex-vivo FACS sorted from bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
total RNA was isolated using a lysis step based on guanidine thiocyanate
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters) (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
ChIP-Seq: Reads were aligned against the Mus musculus genome version of July 2007 (NCBI37/mm9) with the Bowtie program version 0.12.5. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously.
total RNA-Seq: Reads were aligned with STAR version 2.4.2 to the Mus musculus genome version of July 2007 (NCBI37/mm9). Read coverages were calculated with the BEDTool program, were normalized to reads per millions (RPM) using the SAMTools as well as the KentTools.
Assembly: mm9 (total RNA-Seq, RNA-Seq,ChIP-Seq), mm10 (VDJ-Seq)
Supplementary files format and content: tab-delimited text files include RPM values for each VDJ-Seq sample and TPM values for RNA-Seq samples. bigWig files include read coverage for total RNA-Seq and ChIP-Seq samples.
|
| |
|
| Submission date |
Oct 05, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Joris van der Veeken |
| E-mail(s) |
joris.van.der.veeken@imp.ac.at
|
| Organization name |
IMP
|
| Lab |
van der Veeken
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
A-1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE214869 |
Enhancers of the PAIR4 regulatory module promote distal VH gene recombination at the Igh locus |
|
| Relations |
| BioSample |
SAMN31167564 |
| SRA |
SRX17806502 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6617040_187484.cov.all.rpm.bw |
157.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
