B37f1437-f716-479a-8a23-8264673590d4 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001010847 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Whole exome sequencing (the SureSelectXT Mouse All Exon Kit) was done on leukemias from NP23-NHD13 double transgenic mice with strain background designated “C57Bl6-NIH”.
2020-09-10 | GSE137542 | GEO
Project description:This dataset contains paired whole exome sequence data of 5 patients (control/tumor pairs) and paired whole genome sequencing data of 1 patient (control/tumor pair) with Lynch Syndrome from the INFORM registry. Paired sequencing was done mostly on Illumina HiSeq 4000, few on HiSeq2500 and NovaSeq 6000. The library preparation was either with Agilent SureSelect Human_All_Exon V5 (hg19) or with Agilent SureSelectXT HS Human_All_Exon V7 (hg19). The WGS samples were prepared with Agilent SureSelect WGS.
| EGAD00001011098 | EGA
Project description:Primary lymphoma of the central nervous system (PCNSL) is a diffuse large B cell lymphoma confined to the CNS. In order to elucidate its peculiar organ tropism, we generated recombinant antibodies (recAb) identical with the BCR of a series of 23 PCNSL from immunocompetent patients. While none of the recAb showed self-reactivity upon testing with common autoantigens, they recognized 1547 proteins present on a large-scale protein microarray. Interestingly, proteins recognized by the recAb are physiologically expressed by CNS neurons (GRINL1A, centaurin-α, BAIAP2). Furthermore, 87% (20/23) of the recAb including all antibodies derived from IGHV4 34 using PCNSL recognized galectin-3, which was upregulated on microglia/macrophages, astrocytes, and cerebral endothelial cells upon CNS invasion by PCNSL. Thus, PCNSL Ig may recognize CNS proteins as self-antigens. Their interaction may contribute to BCR signaling with sustained NF-κB activation and, ultimately, may foster tumor cell proliferation and survival. These data may also explain, at least in part, the affinity of the tumor cells of PCNSL to the CNS. Recombinant antibodies (recAb) identical with the BCR of a series of 23 PCNSL from immunocompetent patients.
2015-07-01 | E-GEOD-61556 | biostudies-arrayexpress
Project description:Whole-exome sequencing (WES) in a well-characterized sample of 14 matched EP tumour/healthy surrounding tissue samples. The sequencing was done with paired EXOME sequencing on Illumina HiSeq 4000 using Agilent SureSelect XT HS + Human All Exon V7.
| EGAD00001006395 | EGA
Project description:Primary lymphoma of the central nervous system (PCNSL) is a diffuse large B cell lymphoma confined to the CNS. In order to elucidate its peculiar organ tropism, we generated recombinant antibodies (recAb) identical with the BCR of a series of 23 PCNSL from immunocompetent patients. While none of the recAb showed self-reactivity upon testing with common autoantigens, they recognized 1547 proteins present on a large-scale protein microarray. Interestingly, proteins recognized by the recAb are physiologically expressed by CNS neurons (GRINL1A, centaurin-α, BAIAP2). Furthermore, 87% (20/23) of the recAb including all antibodies derived from IGHV4 34 using PCNSL recognized galectin-3, which was upregulated on microglia/macrophages, astrocytes, and cerebral endothelial cells upon CNS invasion by PCNSL. Thus, PCNSL Ig may recognize CNS proteins as self-antigens. Their interaction may contribute to BCR signaling with sustained NF-κB activation and, ultimately, may foster tumor cell proliferation and survival. These data may also explain, at least in part, the affinity of the tumor cells of PCNSL to the CNS.
2015-07-01 | GSE61556 | GEO
Project description:We obtained gene expression data and HD-SNP6.0 copy number data from PTL, PCNSL and PMLBCL samples and performed an integrative analysis on them. RNA was whole genome amplified using Nugen. Gene expression profiles (GEP) and copy number (CN) data were obtained from 7 PTL. GEP was obtained from 15 PCNSL and CN from 23 PCNSL (overlap of 11). The PMLBCL series contained GEP of 9 and CN data from 11 cases (overlap of 9). 180 samples from GSE34171 provide the framework for the CN analysis and are therefore added to the segmented CN file (input_to_gistic.seg.txt).
2015-12-31 | E-GEOD-61578 | biostudies-arrayexpress
Project description:Human PCNSL tumor samples were obtained surgically from clinical patients confirmed by pathology from our hospital. After sample collection processing and suspensions, we performed scRNA-seq following the manufacturer’s protocol. Briefly, the cells were washed with PBS and resuspended in 500 μl PBS. scRNA-seq libraries were prepared using a Chromium Single cell 3’ Reagent kit, version 2. Amplified cDNA and final libraries were evaluated using a High Sensitivity DNA Kit (Agilent Technologies). Sequencing was performed on NovaSeq 6000 (Illumina) at a depth of approximately 400M reads.
2021-09-23 | GSE181304 | GEO
Project description:Whole-exome sequencing data (Agilent SureSelectXT Human All Exon V7). Retrospective study of matched pairs of initial and post-therapeutic GBM cases treated with temozolomide+radiotherapy with a recurrence period greater than one year. Matched normal, initial and post-therapeutic samples for 27 patients and 1 patient (GBM046) with a matched normal and two post-therapeutic samples.
| EGAD00001008568 | EGA
Project description:Purpose: Only a limited number of genetic studies have been performed in primary central nervous system lymphomas (PCNSL), partly due to the rarity of the tumors and the very limited amount of available tissue. In this report, we present the first molecular characterization of copy-number abnormalities (CNA) of newly diagnosed PCNSL by array-based comparative genomic hybridization in formalin fixed paraffin embedded (FFPE) specimens and compare the results with matched frozen tumor specimens. Experimental design: We performed array-based comparative genomic hybridization (aCGH) in FFPE tissues from PCNSL. Results were compared with matched paired frozen tumors. Results: Our analysis confirmed the good to fair quality and reliability of the data generated from limited amounts of tumoral FFPE tissue. Overall, all PCNSL cases were characterized by highly complex karyotypes with a median of 23 copy-number abnormalities (CNA) per patient (range 17-47). Overall, 20 chromosomal regions were recurrently found in more than 40% of cases. Deletions of 6p21, 6q, 9p21.3 and gain of 12q12-q24.33 were the commonest CNA. Other minimal affected regions were defined, and novel recurrent CNAs affecting single genes were identified in 3q26.32 (TBL1XR1) and 8q12.1 (TOX). Conclusions: The results obtained are encouraging. Larger archival tissue collections can now be analyzed in order to complement the still fragmented knowledge we have of the genetic basis of the PCNSL. We included samples from 7 PCNSL patients. In 6 out of these 7 PCNSL patients (cases B – G), aCGH experiments were performed in DNA samples obtained from both snap-frozen and FFPE tissues for assay quality comparative purposes. In the remaining sample (case A), only frozen sample was analyzed.
2012-04-29 | E-GEOD-28952 | biostudies-arrayexpress
Project description:Purpose: Only a limited number of genetic studies have been performed in primary central nervous system lymphomas (PCNSL), partly due to the rarity of the tumors and the very limited amount of available tissue. In this report, we present the first molecular characterization of copy-number abnormalities (CNA) of newly diagnosed PCNSL by array-based comparative genomic hybridization in formalin fixed paraffin embedded (FFPE) specimens and compare the results with matched frozen tumor specimens. Experimental design: We performed array-based comparative genomic hybridization (aCGH) in FFPE tissues from PCNSL. Results were compared with matched paired frozen tumors. Results: Our analysis confirmed the good to fair quality and reliability of the data generated from limited amounts of tumoral FFPE tissue. Overall, all PCNSL cases were characterized by highly complex karyotypes with a median of 23 copy-number abnormalities (CNA) per patient (range 17-47). Overall, 20 chromosomal regions were recurrently found in more than 40% of cases. Deletions of 6p21, 6q, 9p21.3 and gain of 12q12-q24.33 were the commonest CNA. Other minimal affected regions were defined, and novel recurrent CNAs affecting single genes were identified in 3q26.32 (TBL1XR1) and 8q12.1 (TOX). Conclusions: The results obtained are encouraging. Larger archival tissue collections can now be analyzed in order to complement the still fragmented knowledge we have of the genetic basis of the PCNSL.
2012-04-30 | GSE28952 | GEO