|
| Status |
Public on May 01, 2023 |
| Title |
9592 |
| Sample type |
SRA |
| |
|
| Source name |
E2A AB ChIP-Seq Pro-B cell Rag2(-/-)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
chip antibody: E2A Ab (homemade; clone 9296)
cell type: Pro-B cell
genotype: Rag2(-/-)
treatment: 5-days in-vitro expansion
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
ChIP DNA Clean and Concentrator kit (Zymo Research)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
transcriptomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| 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 |
Meinrad Busslinger |
| E-mail(s) |
meinrad.busslinger@imp.ac.at
|
| Organization name |
IMP
|
| Lab |
Busslinger
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
A-1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE214869 |
Enhancers of the PAIR4 regulatory module promote distal VH gene recombination at the Igh locus |
|
| Relations |
| BioSample |
SAMN31167562 |
| SRA |
SRX17806504 |
